diff --git a/README.md b/README.md
index b09cb4f9..1f4ce48c 100644
--- a/README.md
+++ b/README.md
@@ -95,17 +95,16 @@ The script will generate a TSV file with each tool found in the list of GitHub r
 
 1. Run the extraction as explained before
 2. (Optional) Create a text file with ToolShed categories for which tools need to be extracted: 1 ToolShed category per row ([example for microbial data analysis](data/microgalaxy/categories))
-3. (Optional) Create a text file with list of tools to exclude: 1 tool id per row ([example for microbial data analysis](data/microgalaxy/tools_to_exclude))
-4. (Optional) Create a text file with list of tools to really keep (already reviewed): 1 tool id per row ([example for microbial data analysis](data/microgalaxy/tools_to_keep))
+3. (Optional) Create a TSV (tabular) file with 2 columns: ToolShed ids of tool suites (one per line), Boolean with True to keep and False to exclude / 1 tool id per row ([example for microbial data analysis](data/microgalaxy/tools_to_keep_exclude.tsv))
 4. Run the tool extractor script
 
     ```
-    $ python bin/extract_galaxy_tools.py \
+    $ python bin/extract_galaxy_tools.py filtertools \
         --tools <Path to CSV file with all extracted tools> \
-        --filtered_tools <Path to output CSV file with filtered tools> \
+        --ts_filtered_tools <Path to output TSV with tools filtered based on ToolShed category>
+        --filtered_tools <Path to output TSV with filtered tools based on ToolShed category and manual curation> \
         [--categories <Path to ToolShed category file>] \
-        [--excluded <Path to excluded tool file category file>]\
-        [--keep <Path to to-keep tool file category file>]
+        [--keep_exclude <Path to a TSV file with 2 columns: ToolShed ids of tool suites (one per line), Boolean with True to keep and False to exclude>]
     ```
 
 ## Development
diff --git a/bin/extract_galaxy_tools.py b/bin/extract_galaxy_tools.py
index 95a19eb9..6926c264 100644
--- a/bin/extract_galaxy_tools.py
+++ b/bin/extract_galaxy_tools.py
@@ -559,12 +559,14 @@ def export_tools(
     :param output_fp: path to output file
     :param format_list_col: boolean indicating if list columns should be formatting
     """
-    df = pd.DataFrame(tools)
+    df = (
+        pd.DataFrame(tools)
+        .sort_values("Galaxy wrapper id")
+    )
     if format_list_col:
         df["ToolShed categories"] = format_list_column(df["ToolShed categories"])
         df["EDAM operation"] = format_list_column(df["EDAM operation"])
         df["EDAM topic"] = format_list_column(df["EDAM topic"])
-
         df["bio.tool ids"] = format_list_column(df["bio.tool ids"])
 
         # the Galaxy tools need to be formatted for the add_instances_to_table to work
@@ -580,30 +582,31 @@ def export_tools(
 def filter_tools(
     tools: List[Dict],
     ts_cat: List[str],
-    excluded_tools: List[str],
-    keep_tools: List[str],
-) -> List[Dict]:
+    keep_excl_tools: List[Dict],
+) -> tuple:
     """
     Filter tools for specific ToolShed categories and add information if to keep or to exclude
 
     :param tools: dictionary with tools and their metadata
     :param ts_cat: list of ToolShed categories to keep in the extraction
     :param excluded_tools: list of tools to skip
-    :param keep_tools: list of tools to keep
+    :param keep_excl_tools: dictionary with tools and their status (True to keep, False to exclude)
     """
+    ts_filtered_tools = []
     filtered_tools = []
     for tool in tools:
         # filter ToolShed categories and leave function if not in expected categories
         if check_categories(tool["ToolShed categories"], ts_cat):
             name = tool["Galaxy wrapper id"]
-            tool["Reviewed"] = name in keep_tools or name in excluded_tools
-            tool["To keep"] = None
-            if name in keep_tools:
-                tool["To keep"] = True
-            elif name in excluded_tools:
-                tool["To keep"] = False
-            filtered_tools.append(tool)
-    return filtered_tools
+            tool["Reviewed"] = name in keep_excl_tools
+            keep_status = None
+            if name in keep_excl_tools:
+                keep_status = keep_excl_tools[name][1]
+                if keep_status:
+                    filtered_tools.append(tool)
+            tool["To keep"] = keep_status
+            ts_filtered_tools.append(tool)
+    return ts_filtered_tools, filtered_tools
 
 
 if __name__ == "__main__":
@@ -632,15 +635,21 @@ def filter_tools(
     filtertools = subparser.add_parser("filtertools", help="Filter tools")
     filtertools.add_argument(
         "--tools",
-        "-t",
+        "-i",
         required=True,
         help="Filepath to TSV with all extracted tools, generated by extractools command",
     )
+    filtertools.add_argument(
+        "--ts_filtered_tools",
+        "-t",
+        required=True,
+        help="Filepath to TSV with tools filtered based on ToolShed category",
+    )
     filtertools.add_argument(
         "--filtered_tools",
         "-f",
         required=True,
-        help="Filepath to TSV with filtered tools",
+        help="Filepath to TSV with tools filtered based on ToolShed category and manual curation",
     )
     filtertools.add_argument(
         "--categories",
@@ -648,14 +657,9 @@ def filter_tools(
         help="Path to a file with ToolShed category to keep in the extraction (one per line)",
     )
     filtertools.add_argument(
-        "--exclude",
-        "-e",
-        help="Path to a file with ToolShed ids of tools to exclude (one per line)",
-    )
-    filtertools.add_argument(
-        "--keep",
+        "--keep_exclude",
         "-k",
-        help="Path to a file with ToolShed ids of tools to keep (one per line)",
+        help="Path to a TSV file with 2 columns: ToolShed ids of tool suites (one per line), Boolean with True to keep and False to exclude ",
     )
     args = parser.parse_args()
 
@@ -681,11 +685,11 @@ def filter_tools(
         export_tools(tools, args.all_tools, format_list_col=True, add_usage_stats=True)
 
     elif args.command == "filtertools":
-        tools = pd.read_csv(Path(args.tools), sep="\t", keep_default_na=False).to_dict("records")
+        tools = pd.read_csv(args.tools, sep="\t", keep_default_na=False).to_dict("records")
         # get categories and tools to exclude
         categories = read_file(args.categories)
-        excl_tools = read_file(args.exclude)
-        keep_tools = read_file(args.keep)
+        keep_excl_tools = pd.read_csv(args.keep_exclude, sep="\t", index_col=0, header=None).to_dict("index")
         # filter tool lists
-        filtered_tools = filter_tools(tools, categories, excl_tools, keep_tools)
+        ts_filtered_tools, filtered_tools = filter_tools(tools, categories, keep_excl_tools)
+        export_tools(ts_filtered_tools, args.ts_filtered_tools)
         export_tools(filtered_tools, args.filtered_tools)
diff --git a/bin/get_community_tools.sh b/bin/get_community_tools.sh
index b3a6db3a..c6f9faf7 100755
--- a/bin/get_community_tools.sh
+++ b/bin/get_community_tools.sh
@@ -12,10 +12,10 @@ for com_data_fp in data/communities/* ; do
                 python bin/extract_galaxy_tools.py \
                         filtertools \
                         --tools "results/all_tools.tsv" \
+                        --ts_filtered_tools "results/$community/tools_filtered_by_ts_categories.tsv" \
                         --filtered_tools "results/$community/tools.tsv" \
                         --categories "data/communities/$community/categories" \
-                        --exclude "data/communities/$community/tools_to_exclude" \
-                        --keep "data/communities/$community/tools_to_keep"
+                        --keep_exclude "data/communities/$community/tools_to_keep_exclude.tsv"
 
                 python bin/create_interactive_table.py \
                         --table "results/$community/tools.tsv" \
diff --git a/data/communities/imaging/tools_to_keep b/data/communities/imaging/tools_to_keep
deleted file mode 100644
index e69de29b..00000000
diff --git a/data/communities/imaging/tools_to_exclude b/data/communities/imaging/tools_to_keep_exclude.tsv
similarity index 100%
rename from data/communities/imaging/tools_to_exclude
rename to data/communities/imaging/tools_to_keep_exclude.tsv
diff --git a/data/communities/microgalaxy/tools_to_exclude b/data/communities/microgalaxy/tools_to_exclude
deleted file mode 100644
index a66ce6f9..00000000
--- a/data/communities/microgalaxy/tools_to_exclude
+++ /dev/null
@@ -1,512 +0,0 @@
-adapter_removal
-aegean
-AggregateAlignments
-align_back_trans
-AlignCluster
-ampvis2
-anndata
-annotatemyids
-antarna
-aresite2
-arriba
-art
-assembly-stats
-augustus
-augustus
-b2btools
-bam2mappingstats
-bamclipper
-bamhash
-bamparse
-bamtools_filter
-bamtools_split
-bamutil
-barcode_collapse
-baredsc
-barrnap
-bax2bam
-bbtools
-bctools
-bed_to_protein_map
-bellerophon
-best_regression_subsets
-bioinformatics_cafe
-bionano
-bioperl
-biscot
-bismark
-blast_parser
-blast_plus_remote_blastp
-blast_to_scaffold
-blastparser_and_hits
-blastx_to_scaffold
-blastxml_to_gapped_gff3
-blat_coverage_report
-blat_mapping
-blobtoolkit
-blockbuster
-blockclust
-braker
-braker3
-bumbershoot
-bundle_collections
-bwameth
-cactus
-calculate_contrast_threshold
-calisp
-cap3
-cardinal
-cell-types-analysis
-champ_blocs
-charts
-cherri
-chipseeker
-chira
-chromeister
-chromosome_diagram
-circexplorer
-circexplorer2
-clair3
-clc_assembly_cell
-climate-stripes
-CMFinder
-cmsearch_deoverlap
-cmv
-cofold
-colabfold
-colibread
-collapse_collection
-CollectResults
-CollectResultsNoAlign
-combine_tabular_collection
-combineJSON
-compalignp
-compute_motif_frequencies_for_all_motifs
-compute_motifs_frequency
-consensus_from_alignments
-consolidate_vcfs
-coprarna
-count_gff_features
-count_roi_variants
-coverage_report
-coverage_stats
-crispr_studio
-crosscontamination_barcode_filter
-crt
-ctd_batch
-cummerbund
-custom_pro_db
-custom_pro_db_annotation_data_manager
-data_exploration
-data_manager_eggnog_mapper
-data_manager_eggnog_mapper_abspath
-data-hca
-data-scxa
-dbbuilder
-decoyfasta
-deepsig
-delete_overlapping_indels
-deseq2
-deseq2_normalization
-dewseq
-dexseq
-dia_umpire
-dialignr
-diann
-diapysef
-diffacto
-divide_pg_snp
-dorina
-dot2ct
-dotknot
-droplet-barcode-plot
-dropletutils
-dropletutils
-Ecoregionalization_workflow
-edger
-egsea
-emboss_5
-EMLassemblyline
-encyclopedia
-exomedepth
-exonerate
-exparna
-express
-fasta_extract
-fasta_filter_by_id
-fasta_nucleotide_color_plot
-fasta_stats
-fasta2bed
-fastg2protlib
-fastq_filter_by_id
-fastq_pair_names
-fastq_paired_unpaired
-fastq_provider
-fastq_utils
-fastqc_stats
-feature_alignment
-featurecounter
-featurecounts
-feelnc
-feht
-fermikit
-fgsea
-filter_by_fasta_ids
-filter_density
-filter_stats
-filter_transcripts_via_tracking
-filter_vcf
-find_diag_hits
-find_repeats
-fisher_test
-flair
-flash
-flashlfq
-GAFA
-garnett
-gblocks
-gdal
-gecko
-gemini
-geneiobio
-generate_pc_lda_matrix
-genomic_super_signature
-Geom_mean_workflow
-get_orfs_or_cdss
-getindelrates_3way
-getindels_2way
-getorganelle
-gfastats
-gff3_rebase
-gffread
-ggplot2
-gmaj
-gotohscan
-graphclust
-graphprot
-gsc_high_dimensions_visualisation
-GSPAN
-gtf-2-gene-list
-guppy
-gwastools
-hapcut2
-hapog
-hardklor
-hcluster_sg
-hcluster_sg_parser
-heatmap2
-heinz
-helixer
-hgv_fundo
-hgv_hilbertvis
-hicexplorer
-hicstuff
-hifiasm
-high_dim_heatmap
-hisat
-hisat2
-homer
-homer
-htseq_count
-htseq-clip
-hybpiper
-idconvert
-idr
-iedb_api
-illumina_methylation_analyser
-improviser
-indels_3way
-inforna
-instagraal
-intarna
-interpolation
-isoformswitchanalyzer
-isoplot
-jcvi_gff_stats
-kaptive
-kinwalker
-labels
-last
-length_and_gc_content
-lfq_protein_quant
-limma_voom
-links
-locarna
-LocARNAGraphClust
-logistic_regression_vif
-logol
-macs2
-maf_cpg_filter
-maldiquant
-map_peptides_to_bed
-mapping_quality_stats
-mapping_to_ucsc
-mashmap
-masigpro
-mauve_contig_mover
-maxquant
-mea
-mean-per-zone
-medenv
-meta_proteome_analyzer
-metanovo
-metaquantome
-methtools
-methyldackel
-metilene
-miclip
-microsatellite_birthdeath
-microsats_alignment_level
-microsats_mutability
-migmap
-minced
-miranda
-mircounts
-mirmachine
-mirnature
-mitobim
-mitohifi
-moFF
-monocle3
-morpheus
-mqc
-mqppep
-msconvert
-msgfplus
-msms_extractor
-msstats
-msstatstmt
-mt2mq
-multispecies_orthologous_microsats
-mummer
-mummer4
-mz_to_sqlite
-mzml_validator
-naltorfs
-nastiseq
-ncbi_fcs_adaptor
-necat
-nlstradamus
-novoplasty
-NSPDK
-oases
-ocean
-odgi
-ogcProcess_otb_bandmath
-ogcProcess_otb_meanShiftSmoothing
-ont_fast5_api
-openms
-openms
-optitype
-pairtools
-pangolin
-pangolin
-paralyzer
-parse_mito_blast
-pathview
-pathwaymatcher
-patrist
-peakachu
-pep_pointer
-pepquery
-pepquery2
-peptide_genomic_coordinate
-peptideshaker
-peptimapper
-pepxml_to_xls
-percolator
-pi_db_tools
-pipmir
-piranha
-plasmid_profiler_suite
-platypus
-plotly_ml_performance_plots
-plotly_parallel_coordinates_plot
-plotly_regression_performance_plots
-Plotting
-pmd_fdr
-poisson2test
-predictnls
-PrepareForMlocarna
-Preprocessing
-presto
-pretext
-prinseq
-probecoverage
-progressivemauve
-prot-scriber
-protease_prediction
-protein_analysis
-protein_properties
-proteomiqon_joinquantpepionswithproteins
-proteomiqon_labeledproteinquantification
-proteomiqon_labelfreeproteinquantification
-proteomiqon_mzmltomzlite
-proteomiqon_peptidedb
-proteomiqon_peptidespectrummatching
-proteomiqon_proteininference
-proteomiqon_psmbasedquantification
-proteomiqon_psmstatistics
-proteore_venn_diagram
-pseudogenome
-psm_validation
-psm2sam
-psy-maps
-pureclip
-purge_dups
-pyprophet
-pysradb
-pyteomics
-qq_tools
-quality_filter
-quantp
-quantwiz_iq
-quasitools
-ragtag
-rapidnj
-raven
-rawtools
-rbpbench
-rcas
-rcve
-red
-refseq_masher
-regionalgam
-remurna
-repeat_masker
-repeatmasker
-repeatmodeler
-revoluzer
-ribotaper
-ribowaltz
-rna_shapes
-rnabob
-rnacode
-rnacommender
-rnalien
-rnaquast
-rnasnp
-rnaz
-rsem
-ruvseq
-sailfish
-salmon-kallisto-mtx-to-10x
-salsa2
-sample_seqs
-samtools_depad
-samtools_depth
-samtools_idxstats
-sashimi_plot
-sc3
-scanpy
-scanpy
-scater
-scater
-schicexplorer
-scikit-bio
-scmap
-scpipe
-scpred
-sdmpredictors
-selectsequencesfrommsa
-seq_composition
-seq_filter_by_id
-seq_filter_by_mapping
-seq_length
-seq_primer_clip
-seq_rename
-seq_select_by_id
-seq2hla
-seqcomplexity
-seqtk
-seqtk_nml
-seqwish
-seurat
-seurat
-shasta
-short_reads_figure_high_quality_length
-short_reads_figure_score
-sickle
-sina
-sinto
-sixgill
-slamdunk
-sleuth
-small_rna_clusters
-small_rna_maps
-small_rna_signatures
-smart_domains
-smudgeplot
-sniffles
-snipit
-snv_matrix
-socru
-spaln
-spatyper
-spectrast2spectrast_irt
-spectrast2tsv
-spocc
-spolpred
-sr_bowtie
-sr_bowtie_dataset_annotation
-srs_tools
-sshmm
-stacks
-stacks2
-star_fusion
-stoc
-Structure_GSPAN
-structureharvester
-substitution_rates
-substitutions
-suite_snvphyl
-syndiva
-tapscan
-tarfast5
-targetfinder
-tasmanian_mismatch
-taxonomy_filter_refseq
-tbl2gff3
-te_finder
-telescope
-tetoolkit
-tetyper
-tgsgapcloser
-ThermoRawFileParser
-tn93
-tophat
-tophat2
-transdecoder
-translate_bed
-translate_bed_sequences
-TrimNs
-trinity
-trinotate
-trna_prediction
-tsebra
-ucsc_blat
-ucsc_custom_track
-umi_tools
-unipept
-uniprot_rest_interface
-uniprotxml_downloader
-validate_fasta_database
-vcf2snvalignment
-venn_list
-verify_map
-verkko
-vg
-vienna_rna
-vigiechiro
-volcanoplot
-vsnp
-vt
-wade
-weather_app
-weightedaverage
-windowmasker
-windowsplitter
-xarray
-xpore
-yac_clipper
-yahs
\ No newline at end of file
diff --git a/data/communities/microgalaxy/tools_to_keep b/data/communities/microgalaxy/tools_to_keep
deleted file mode 100644
index 02a1e956..00000000
--- a/data/communities/microgalaxy/tools_to_keep
+++ /dev/null
@@ -1,313 +0,0 @@
-abacas
-abricate
-abritamr
-abyss
-aldex2
-amplican
-amrfinderplus
-ancombc
-antismash
-apollo
-artic
-assemblystats
-bakta
-bamtools
-bandage
-bayescan
-bbtools
-bcftools
-bedtools
-bigscape
-binning_refiner
-biohansel
-biom_format
-biotradis
-blast_rbh
-blast2go
-blastxml_to_top_descr
-bracken
-busco
-bwa
-cat
-cd_hit_dup
-cdhit
-cemitool
-checkm
-chopin2
-circos
-clair3
-clinod
-clustalw
-cmsearch_deoverlap
-codeml
-cojac
-combine_assembly_stats
-combine_metaphlan_humann
-compare_humann2_output
-compleasm
-concoct
-coverm
-cryptogenotyper
-cutadapt
-dada2
-das_tool
-datamash
-deepmicro
-deseq2
-diamond
-disco
-dram
-drep
-ectyper
-effectiveT3
-eggnog_mapper
-emboss_5
-ete
-export2graphlan
-ez_histograms
-fargene
-fasta_merge_files_and_filter_unique_sequences
-fastani
-fastp
-fastqc
-fastqe
-fasttree
-featurecounts
-filter_spades_repeats
-filtlong
-flashlfq
-flye
-format_metaphlan2_output
-fraggenescan
-freebayes
-freyja
-frogs
-funannotate
-getmlst
-ggplot2
-gi2taxonomy
-glimmer
-glimmer_hmm
-goenrichment
-goseq
-graphlan
-graphmap
-gtdbtk
-gubbins
-hamronization
-hansel
-hifiasm_meta
-hivtrace
-hmmer3
-humann
-hyphy
-hypo
-icescreen
-idba_ud
-infernal
-instrain
-integron_finder
-interproscan
-iprscan5
-iqtree
-isescan
-itsx
-ivar
-jbrowse
-jellyfish
-kallisto
-kat_filter
-kc-align
-khmer
-kleborate
-kma
-kofamscan
-kraken
-kraken_biom
-kraken_taxonomy_report
-kraken2
-kraken2tax
-krakentools
-krocus
-lastz_paired_reads
-lca_wrapper
-legsta
-lighter
-limma_voom
-lineagespot
-lorikeet
-lotus2
-m6anet
-maaslin2
-mafft
-make_nr
-maker
-mapseq
-mash
-maxbin2
-maxquant
-mcl
-medaka
-megahit
-megahit_contig2fastg
-megan
-meningotype
-merqury
-meryl
-metabat2
-metaeuk
-metagene_annotator
-metagenomeseq
-metanovo
-metaphlan
-metaquantome
-metawrapmg
-minia
-miniasm
-minimap2
-minipolish
-miniprot
-mitos
-mlst
-mob_suite
-mothur
-mrbayes
-msconvert
-msstatstmt
-multigsea
-multiqc
-mykrobe
-mykrobe_parser
-mz_to_sqlite
-nanocompore
-nanoplot
-nanopolishcomp
-ncbi_blast_plus
-ncbi_fcs_gx
-newick_utils
-nextclade
-nextdenovo
-nonpareil
-nucleosome_prediction
-nugen_nudup
-obisindicators
-obitools
-orfipy
-orthofinder
-omark
-PAMPA
-peptideshaker
-pfamscan
-pharokka
-phyloseq
-phyml
-picard
-picrust
-picrust2
-plasflow
-plasmidfinder
-plasmidspades
-polypolish
-porechop
-prodigal
-prokka
-promer
-proteinortho
-pycoqc
-pygenometracks
-qiime_add_on
-qiime_core
-qualimap
-quast
-query_tabular
-quickmerge
-racon
-rasusa
-raxml
-read_it_and_keep
-reago
-recentrifuge
-repeatexplorer2
-rgrnastar
-roary
-rRNA
-rseqc
-salmon
-samtools
-sarscov2formatter
-sarscov2summary
-scoary
-semibin
-seqkit
-seqprep
-seqsero2
-shorah
-shovill
-sistr_cmd
-sklearn
-smallgenomeutilities
-smalt
-snap
-snippy
-snp-dists
-snp-sites
-snpsift
-sonneityping
-sortmerna
-spades
-spotyping
-sr_bowtie
-srst2
-staramr
-stringmlst
-structure
-suite_qiime2__alignment
-suite_qiime2__composition
-suite_qiime2__cutadapt
-suite_qiime2__dada2
-suite_qiime2__deblur
-suite_qiime2__demux
-suite_qiime2__diversity
-suite_qiime2__diversity_lib
-suite_qiime2__emperor
-suite_qiime2__feature_classifier
-suite_qiime2__feature_table
-suite_qiime2__fragment_insertion
-suite_qiime2__gneiss
-suite_qiime2__longitudinal
-suite_qiime2__metadata
-suite_qiime2__phylogeny
-suite_qiime2__quality_control
-suite_qiime2__quality_filter
-suite_qiime2__sample_classifier
-suite_qiime2__taxa
-suite_qiime2__vsearch
-suite_qiime2_core__tools
-suite_qiime2_core
-t_coffee
-t2ps
-t2t_report
-taxonomy_krona_chart
-tb_variant_filter
-tb-profiler
-transit
-transtermhp
-TreeBest
-trim_galore
-trimmomatic
-trycycler
-unicycler
-unipept
-uniprotxml_downloader
-usher
-valet
-vapor
-varvamp
-vcffilter
-vcfprimers
-vegan
-velvet
-velvet_optimiser
-virAnnot
-vsearch
-wtdbg
\ No newline at end of file
diff --git a/data/communities/microgalaxy/tools_to_keep_exclude.tsv b/data/communities/microgalaxy/tools_to_keep_exclude.tsv
new file mode 100644
index 00000000..25371632
--- /dev/null
+++ b/data/communities/microgalaxy/tools_to_keep_exclude.tsv
@@ -0,0 +1,773 @@
+abacas	TRUE
+abricate	TRUE
+abritamr	TRUE
+abyss	TRUE
+adapter_removal	FALSE
+aegean	FALSE
+AggregateAlignments	FALSE
+aldex2	TRUE
+align_back_trans	FALSE
+AlignCluster	FALSE
+amplican	TRUE
+ampvis2	FALSE
+amrfinderplus	TRUE
+ancombc	TRUE
+anndata	FALSE
+annotatemyids	FALSE
+antarna	FALSE
+antismash	TRUE
+aresite2	FALSE
+arriba	FALSE
+art	FALSE
+artic	TRUE
+assembly-stats	FALSE
+assemblystats	TRUE
+augustus	FALSE
+b2btools	FALSE
+bakta	TRUE
+bam2mappingstats	FALSE
+bamclipper	FALSE
+bamhash	FALSE
+bamparse	FALSE
+bamtools	TRUE
+bamtools_filter	FALSE
+bamtools_split	FALSE
+bamutil	FALSE
+bandage	TRUE
+barcode_collapse	FALSE
+baredsc	FALSE
+barrnap	FALSE
+bax2bam	FALSE
+bayescan	TRUE
+bbtools	TRUE
+bctools	FALSE
+bed_to_protein_map	FALSE
+bellerophon	FALSE
+best_regression_subsets	FALSE
+bigscape	TRUE
+binning_refiner	TRUE
+biohansel	TRUE
+bioinformatics_cafe	FALSE
+biom_format	TRUE
+bionano	FALSE
+bioperl	FALSE
+biotradis	TRUE
+biscot	FALSE
+bismark	FALSE
+blast_parser	FALSE
+blast_plus_remote_blastp	FALSE
+blast_rbh	TRUE
+blast_to_scaffold	FALSE
+blast2go	TRUE
+blastparser_and_hits	FALSE
+blastx_to_scaffold	FALSE
+blastxml_to_gapped_gff3	FALSE
+blastxml_to_top_descr	TRUE
+blat_coverage_report	FALSE
+blat_mapping	FALSE
+blobtoolkit	FALSE
+blockbuster	FALSE
+blockclust	FALSE
+bracken	TRUE
+braker	FALSE
+braker3	FALSE
+bumbershoot	FALSE
+bundle_collections	FALSE
+busco	TRUE
+bwameth	FALSE
+cactus	FALSE
+calculate_contrast_threshold	FALSE
+calisp	FALSE
+cap3	FALSE
+cardinal	FALSE
+cat	TRUE
+cd_hit_dup	TRUE
+cdhit	TRUE
+cell-types-analysis	FALSE
+cemitool	TRUE
+champ_blocs	FALSE
+charts	FALSE
+checkm	TRUE
+cherri	FALSE
+chipseeker	FALSE
+chira	FALSE
+chromeister	FALSE
+chromosome_diagram	FALSE
+circexplorer	FALSE
+circexplorer2	FALSE
+clair3	TRUE
+clc_assembly_cell	FALSE
+climate-stripes	FALSE
+clinod	TRUE
+clustalw	TRUE
+CMFinder	FALSE
+cmsearch_deoverlap	TRUE
+cmv	FALSE
+codeml	TRUE
+cofold	FALSE
+cojac	TRUE
+colabfold	FALSE
+colibread	FALSE
+collapse_collection	FALSE
+CollectResults	FALSE
+CollectResultsNoAlign	FALSE
+combine_assembly_stats	TRUE
+combine_metaphlan_humann	TRUE
+combine_tabular_collection	FALSE
+combineJSON	FALSE
+compalignp	FALSE
+compare_humann2_output	TRUE
+compleasm	TRUE
+compute_motif_frequencies_for_all_motifs	FALSE
+compute_motifs_frequency	FALSE
+concoct	TRUE
+consensus_from_alignments	FALSE
+consolidate_vcfs	FALSE
+coprarna	FALSE
+count_gff_features	FALSE
+count_roi_variants	FALSE
+coverage_report	FALSE
+coverage_stats	FALSE
+coverm	TRUE
+crispr_studio	FALSE
+crosscontamination_barcode_filter	FALSE
+crt	FALSE
+cryptogenotyper	TRUE
+ctd_batch	FALSE
+cummerbund	FALSE
+custom_pro_db	FALSE
+custom_pro_db_annotation_data_manager	FALSE
+cutadapt	TRUE
+dada2	TRUE
+das_tool	TRUE
+data_exploration	FALSE
+data_manager_eggnog_mapper	FALSE
+data_manager_eggnog_mapper_abspath	FALSE
+data-hca	FALSE
+data-scxa	FALSE
+dbbuilder	FALSE
+decoyfasta	FALSE
+deepsig	FALSE
+delete_overlapping_indels	FALSE
+deseq2	TRUE
+deseq2_normalization	FALSE
+dewseq	FALSE
+dexseq	FALSE
+dia_umpire	FALSE
+dialignr	FALSE
+diamond	TRUE
+diann	FALSE
+diapysef	FALSE
+diffacto	FALSE
+disco	TRUE
+divide_pg_snp	FALSE
+dorina	FALSE
+dot2ct	FALSE
+dotknot	FALSE
+dram	TRUE
+drep	TRUE
+droplet-barcode-plot	FALSE
+dropletutils	FALSE
+Ecoregionalization_workflow	FALSE
+ectyper	TRUE
+edger	FALSE
+effectiveT3	TRUE
+eggnog_mapper	TRUE
+egsea	FALSE
+emboss_5	TRUE
+EMLassemblyline	FALSE
+encyclopedia	FALSE
+ete	TRUE
+exomedepth	FALSE
+exonerate	FALSE
+exparna	FALSE
+export2graphlan	TRUE
+express	FALSE
+ez_histograms	TRUE
+fargene	TRUE
+fasta_extract	FALSE
+fasta_filter_by_id	FALSE
+fasta_nucleotide_color_plot	FALSE
+fasta_stats	FALSE
+fasta2bed	FALSE
+fastani	TRUE
+fastg2protlib	FALSE
+fastk	TRUE
+fastp	TRUE
+fastq_filter_by_id	FALSE
+fastq_pair_names	FALSE
+fastq_paired_unpaired	FALSE
+fastq_provider	FALSE
+fastq_utils	FALSE
+fastqc_stats	FALSE
+fastqe	TRUE
+fasttree	TRUE
+feature_alignment	FALSE
+featurecounter	FALSE
+featurecounts	TRUE
+feelnc	FALSE
+feht	FALSE
+fermikit	FALSE
+fgsea	FALSE
+filter_by_fasta_ids	FALSE
+filter_density	FALSE
+filter_spades_repeats	TRUE
+filter_stats	FALSE
+filter_transcripts_via_tracking	FALSE
+filter_vcf	FALSE
+filtlong	TRUE
+find_diag_hits	FALSE
+find_repeats	FALSE
+fisher_test	FALSE
+flair	FALSE
+flash	FALSE
+flashlfq	TRUE
+flye	TRUE
+format_metaphlan2_output	TRUE
+fraggenescan	TRUE
+freyja	TRUE
+frogs	TRUE
+funannotate	TRUE
+GAFA	FALSE
+garnett	FALSE
+gblocks	FALSE
+gdal	FALSE
+gecko	FALSE
+gemini	FALSE
+geneiobio	FALSE
+generate_pc_lda_matrix	FALSE
+genomic_super_signature	FALSE
+Geom_mean_workflow	FALSE
+get_orfs_or_cdss	FALSE
+getindelrates_3way	FALSE
+getindels_2way	FALSE
+getmlst	TRUE
+getorganelle	FALSE
+gfastats	FALSE
+gff3_rebase	FALSE
+gffread	FALSE
+ggplot2	TRUE
+gi2taxonomy	TRUE
+glimmer	TRUE
+glimmer_hmm	TRUE
+gmaj	FALSE
+goenrichment	TRUE
+goseq	TRUE
+gotohscan	FALSE
+graphclust	FALSE
+graphlan	TRUE
+graphmap	TRUE
+graphprot	FALSE
+gsc_high_dimensions_visualisation	FALSE
+GSPAN	FALSE
+gtdbtk	TRUE
+gtf-2-gene-list	FALSE
+gubbins	TRUE
+guppy	FALSE
+gwastools	FALSE
+hamronization	TRUE
+hansel	TRUE
+hapcut2	FALSE
+hapog	FALSE
+hardklor	FALSE
+hcluster_sg	FALSE
+hcluster_sg_parser	FALSE
+heatmap2	FALSE
+heinz	FALSE
+helixer	FALSE
+hgv_fundo	FALSE
+hgv_hilbertvis	FALSE
+hicexplorer	FALSE
+hicstuff	FALSE
+hifiasm	FALSE
+hifiasm_meta	TRUE
+high_dim_heatmap	FALSE
+hisat	FALSE
+hisat2	FALSE
+hivtrace	TRUE
+hmmer3	TRUE
+homer	FALSE
+htseq_count	FALSE
+htseq-clip	FALSE
+humann	TRUE
+hybpiper	FALSE
+hyphy	TRUE
+hypo	TRUE
+icescreen	TRUE
+idba_ud	TRUE
+idconvert	FALSE
+idr	FALSE
+iedb_api	FALSE
+illumina_methylation_analyser	FALSE
+improviser	FALSE
+indels_3way	FALSE
+infernal	TRUE
+inforna	FALSE
+instagraal	FALSE
+instrain	TRUE
+intarna	FALSE
+integron_finder	TRUE
+interpolation	FALSE
+interproscan	TRUE
+iprscan5	TRUE
+iqtree	TRUE
+isescan	TRUE
+isoformswitchanalyzer	FALSE
+isoplot	FALSE
+itsx	TRUE
+ivar	TRUE
+jbrowse	TRUE
+jcvi_gff_stats	FALSE
+jellyfish	TRUE
+kaptive	FALSE
+kat_filter	TRUE
+kc-align	TRUE
+khmer	TRUE
+kinwalker	FALSE
+kleborate	TRUE
+kofamscan	TRUE
+kraken	TRUE
+kraken_biom	TRUE
+kraken_taxonomy_report	TRUE
+kraken2	TRUE
+kraken2tax	TRUE
+krakentools	TRUE
+krocus	TRUE
+labels	FALSE
+last	FALSE
+lca_wrapper	TRUE
+legsta	TRUE
+length_and_gc_content	FALSE
+lfq_protein_quant	FALSE
+lighter	TRUE
+limma_voom	TRUE
+lineagespot	TRUE
+links	FALSE
+locarna	FALSE
+LocARNAGraphClust	FALSE
+logistic_regression_vif	FALSE
+logol	FALSE
+lorikeet	TRUE
+lotus2	TRUE
+m6anet	TRUE
+maaslin2	TRUE
+macs2	FALSE
+maf_cpg_filter	FALSE
+mafft	TRUE
+make_nr	TRUE
+maker	TRUE
+maldiquant	FALSE
+map_peptides_to_bed	FALSE
+mapping_quality_stats	FALSE
+mapping_to_ucsc	FALSE
+mapseq	TRUE
+mash	TRUE
+mashmap	FALSE
+masigpro	FALSE
+mauve_contig_mover	FALSE
+maxbin2	TRUE
+maxquant	TRUE
+mcl	TRUE
+mea	FALSE
+mean-per-zone	FALSE
+medaka	TRUE
+medenv	FALSE
+megahit	TRUE
+megahit_contig2fastg	TRUE
+megan	TRUE
+meningotype	TRUE
+merqury	TRUE
+meryl	TRUE
+meta_proteome_analyzer	FALSE
+metabat2	TRUE
+metaeuk	TRUE
+metagene_annotator	TRUE
+metagenomeseq	TRUE
+metanovo	TRUE
+metaphlan	TRUE
+metaquantome	TRUE
+metawrapmg	TRUE
+methtools	FALSE
+methyldackel	FALSE
+metilene	FALSE
+miclip	FALSE
+microsatellite_birthdeath	FALSE
+microsats_alignment_level	FALSE
+microsats_mutability	FALSE
+migmap	FALSE
+minced	FALSE
+minia	TRUE
+miniasm	TRUE
+minipolish	TRUE
+miniprot	TRUE
+miranda	FALSE
+mircounts	FALSE
+mirmachine	FALSE
+mirnature	FALSE
+mitobim	FALSE
+mitohifi	FALSE
+mitos	TRUE
+mlst	TRUE
+mob_suite	TRUE
+moFF	FALSE
+monocle3	FALSE
+morpheus	FALSE
+mothur	TRUE
+mqc	FALSE
+mqppep	FALSE
+mrbayes	TRUE
+msconvert	TRUE
+msgfplus	FALSE
+msms_extractor	FALSE
+msstats	FALSE
+msstatstmt	TRUE
+mt2mq	FALSE
+multigsea	TRUE
+multiqc	TRUE
+multispecies_orthologous_microsats	FALSE
+mummer	FALSE
+mummer4	FALSE
+mykrobe	TRUE
+mykrobe_parser	TRUE
+mz_to_sqlite	TRUE
+mzml_validator	FALSE
+naltorfs	FALSE
+nanocompore	TRUE
+nanoplot	TRUE
+nanopolishcomp	TRUE
+nastiseq	FALSE
+ncbi_blast_plus	TRUE
+ncbi_fcs_adaptor	FALSE
+ncbi_fcs_gx	TRUE
+necat	FALSE
+newick_utils	TRUE
+nextclade	TRUE
+nextdenovo	TRUE
+nlstradamus	FALSE
+nonpareil	TRUE
+novoplasty	FALSE
+NSPDK	FALSE
+nucleosome_prediction	TRUE
+nugen_nudup	TRUE
+oases	FALSE
+obisindicators	TRUE
+obitools	TRUE
+ocean	FALSE
+odgi	FALSE
+ogcProcess_otb_bandmath	FALSE
+ogcProcess_otb_meanShiftSmoothing	FALSE
+omark	TRUE
+ont_fast5_api	FALSE
+openms	FALSE
+optitype	FALSE
+orfipy	TRUE
+orthofinder	TRUE
+pairtools	FALSE
+PAMPA	TRUE
+pangolin	FALSE
+paralyzer	FALSE
+parse_mito_blast	FALSE
+pathview	FALSE
+pathwaymatcher	FALSE
+patrist	FALSE
+peakachu	FALSE
+pep_pointer	FALSE
+pepquery	FALSE
+pepquery2	FALSE
+peptide_genomic_coordinate	FALSE
+peptideshaker	TRUE
+peptimapper	FALSE
+pepxml_to_xls	FALSE
+percolator	FALSE
+pfamscan	TRUE
+pharokka	TRUE
+phyloseq	TRUE
+phyml	TRUE
+pi_db_tools	FALSE
+picrust	TRUE
+picrust2	TRUE
+pipmir	FALSE
+piranha	FALSE
+plasflow	TRUE
+plasmid_profiler_suite	FALSE
+plasmidfinder	TRUE
+plasmidspades	TRUE
+platypus	FALSE
+plotly_ml_performance_plots	FALSE
+plotly_parallel_coordinates_plot	FALSE
+plotly_regression_performance_plots	FALSE
+Plotting	FALSE
+pmd_fdr	FALSE
+poisson2test	FALSE
+polypolish	TRUE
+predictnls	FALSE
+PrepareForMlocarna	FALSE
+Preprocessing	FALSE
+presto	FALSE
+pretext	FALSE
+prinseq	FALSE
+probecoverage	FALSE
+prodigal	TRUE
+progressivemauve	FALSE
+prokka	TRUE
+promer	TRUE
+prot-scriber	FALSE
+protease_prediction	FALSE
+protein_analysis	FALSE
+protein_properties	FALSE
+proteinortho	TRUE
+proteomiqon_joinquantpepionswithproteins	FALSE
+proteomiqon_labeledproteinquantification	FALSE
+proteomiqon_labelfreeproteinquantification	FALSE
+proteomiqon_mzmltomzlite	FALSE
+proteomiqon_peptidedb	FALSE
+proteomiqon_peptidespectrummatching	FALSE
+proteomiqon_proteininference	FALSE
+proteomiqon_psmbasedquantification	FALSE
+proteomiqon_psmstatistics	FALSE
+proteore_venn_diagram	FALSE
+pseudogenome	FALSE
+psm_validation	FALSE
+psm2sam	FALSE
+psy-maps	FALSE
+pureclip	FALSE
+purge_dups	FALSE
+pycoqc	TRUE
+pygenometracks	TRUE
+pyprophet	FALSE
+pysradb	FALSE
+pyteomics	FALSE
+qiime_add_on	TRUE
+qiime_core	TRUE
+qq_tools	FALSE
+qualimap	TRUE
+quality_filter	FALSE
+quantp	FALSE
+quantwiz_iq	FALSE
+quasitools	FALSE
+quast	TRUE
+quickmerge	TRUE
+racon	TRUE
+ragtag	FALSE
+rapidnj	FALSE
+rasusa	TRUE
+raven	FALSE
+rawtools	FALSE
+raxml	TRUE
+rbpbench	FALSE
+rcas	FALSE
+rcve	FALSE
+read_it_and_keep	TRUE
+reago	TRUE
+recentrifuge	TRUE
+red	FALSE
+refseq_masher	FALSE
+regionalgam	FALSE
+remurna	FALSE
+repeat_masker	FALSE
+repeatexplorer2	TRUE
+repeatmasker	FALSE
+repeatmodeler	FALSE
+revoluzer	FALSE
+ribotaper	FALSE
+ribowaltz	FALSE
+rna_shapes	FALSE
+rnabob	FALSE
+rnacode	FALSE
+rnacommender	FALSE
+rnalien	FALSE
+rnaquast	FALSE
+rnasnp	FALSE
+rnaz	FALSE
+roary	TRUE
+rRNA	TRUE
+rsem	FALSE
+rseqc	TRUE
+ruvseq	FALSE
+sailfish	FALSE
+salmon	TRUE
+salmon-kallisto-mtx-to-10x	FALSE
+salsa2	FALSE
+sample_seqs	FALSE
+samtools_depad	FALSE
+samtools_depth	FALSE
+samtools_idxstats	FALSE
+sarscov2formatter	TRUE
+sarscov2summary	TRUE
+sashimi_plot	FALSE
+sc3	FALSE
+scanpy	FALSE
+scater	FALSE
+schicexplorer	FALSE
+scikit-bio	FALSE
+scmap	FALSE
+scoary	TRUE
+scpipe	FALSE
+scpred	FALSE
+sdmpredictors	FALSE
+selectsequencesfrommsa	FALSE
+semibin	TRUE
+seq_composition	FALSE
+seq_filter_by_id	FALSE
+seq_filter_by_mapping	FALSE
+seq_length	FALSE
+seq_primer_clip	FALSE
+seq_rename	FALSE
+seq_select_by_id	FALSE
+seq2hla	FALSE
+seqcomplexity	FALSE
+seqkit	TRUE
+seqprep	TRUE
+seqsero2	TRUE
+seqtk	FALSE
+seqtk_nml	FALSE
+seqwish	FALSE
+seurat	FALSE
+shasta	FALSE
+shorah	TRUE
+short_reads_figure_high_quality_length	FALSE
+short_reads_figure_score	FALSE
+shovill	TRUE
+sickle	FALSE
+sina	FALSE
+sinto	FALSE
+sistr_cmd	TRUE
+sixgill	FALSE
+slamdunk	FALSE
+sleuth	FALSE
+small_rna_clusters	FALSE
+small_rna_maps	FALSE
+small_rna_signatures	FALSE
+smallgenomeutilities	TRUE
+smalt	TRUE
+smart_domains	FALSE
+smudgeplot	FALSE
+snap	TRUE
+sniffles	FALSE
+snipit	FALSE
+snippy	TRUE
+snv_matrix	FALSE
+socru	FALSE
+sonneityping	TRUE
+sortmerna	TRUE
+spades	TRUE
+spaln	FALSE
+spatyper	FALSE
+spectrast2spectrast_irt	FALSE
+spectrast2tsv	FALSE
+spocc	FALSE
+spolpred	FALSE
+spotyping	TRUE
+sr_bowtie	TRUE
+sr_bowtie_dataset_annotation	FALSE
+srs_tools	FALSE
+srst2	TRUE
+sshmm	FALSE
+stacks	FALSE
+stacks2	FALSE
+star_fusion	FALSE
+staramr	TRUE
+stoc	FALSE
+stringmlst	TRUE
+structure	TRUE
+Structure_GSPAN	FALSE
+structureharvester	FALSE
+substitution_rates	FALSE
+substitutions	FALSE
+suite_qiime2__alignment	TRUE
+suite_qiime2__composition	TRUE
+suite_qiime2__cutadapt	TRUE
+suite_qiime2__dada2	TRUE
+suite_qiime2__deblur	TRUE
+suite_qiime2__demux	TRUE
+suite_qiime2__diversity	TRUE
+suite_qiime2__diversity_lib	TRUE
+suite_qiime2__emperor	TRUE
+suite_qiime2__feature_classifier	TRUE
+suite_qiime2__feature_table	TRUE
+suite_qiime2__fragment_insertion	TRUE
+suite_qiime2__longitudinal	TRUE
+suite_qiime2__metadata	TRUE
+suite_qiime2__phylogeny	TRUE
+suite_qiime2__quality_control	TRUE
+suite_qiime2__quality_filter	TRUE
+suite_qiime2__rescript	TRUE
+suite_qiime2__sample_classifier	TRUE
+suite_qiime2__taxa	TRUE
+suite_qiime2__vsearch	TRUE
+suite_qiime2_core	TRUE
+suite_qiime2_core__tools	TRUE
+suite_snvphyl	FALSE
+syndiva	FALSE
+t_coffee	TRUE
+t2ps	TRUE
+t2t_report	TRUE
+tapscan	FALSE
+tarfast5	FALSE
+targetfinder	FALSE
+tasmanian_mismatch	FALSE
+taxonomy_filter_refseq	FALSE
+taxonomy_krona_chart	TRUE
+tb-profiler	TRUE
+tbl2gff3	FALSE
+te_finder	FALSE
+telescope	FALSE
+tetoolkit	FALSE
+tetyper	FALSE
+tgsgapcloser	FALSE
+ThermoRawFileParser	FALSE
+tn93	FALSE
+tooldistillator	TRUE
+tophat	FALSE
+tophat2	FALSE
+transdecoder	FALSE
+transit	TRUE
+translate_bed	FALSE
+translate_bed_sequences	FALSE
+transtermhp	TRUE
+TreeBest	TRUE
+trim_galore	TRUE
+TrimNs	FALSE
+trinity	FALSE
+trinotate	FALSE
+trna_prediction	FALSE
+trycycler	TRUE
+tsebra	FALSE
+ucsc_blat	FALSE
+ucsc_custom_track	FALSE
+umi_tools	FALSE
+unicycler	TRUE
+unipept	TRUE
+uniprot_rest_interface	FALSE
+uniprotxml_downloader	TRUE
+usher	TRUE
+valet	TRUE
+validate_fasta_database	FALSE
+vapor	TRUE
+varvamp	TRUE
+vcf2snvalignment	FALSE
+vegan	TRUE
+velvet	TRUE
+velvet_optimiser	TRUE
+venn_list	FALSE
+verify_map	FALSE
+verkko	FALSE
+vg	FALSE
+vienna_rna	FALSE
+vigiechiro	FALSE
+virAnnot	TRUE
+volcanoplot	FALSE
+vsearch	TRUE
+vsnp	FALSE
+vt	FALSE
+wade	FALSE
+weather_app	FALSE
+weightedaverage	FALSE
+windowmasker	FALSE
+windowsplitter	FALSE
+wtdbg	TRUE
+xarray	FALSE
+xpore	FALSE
+yac_clipper	FALSE
+yahs	FALSE
+zoo_project_ogc_api_processes	FALSE
\ No newline at end of file
diff --git a/results/microgalaxy/tools.tsv b/results/microgalaxy/tools.tsv
index 7176845d..df28352e 100644
--- a/results/microgalaxy/tools.tsv
+++ b/results/microgalaxy/tools.tsv
@@ -1,470 +1,144 @@
 Galaxy wrapper id	Total tool usage (usegalaxy.eu)	No. of tool users (2022-2023) (usegalaxy.eu)	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	https://usegalaxy.org	https://usegalaxy.org.au	https://usegalaxy.eu	https://usegalaxy.fr	Reviewed	To keep
-braker	109.0	17.0	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6			(0/1)	(0/1)	(1/1)	(0/1)	True	False
-braker3	567.0	10.0	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			(0/1)	(1/1)	(1/1)	(1/1)	True	False
-helixer	93.0	1.0	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			(0/1)	(0/1)	(1/1)	(1/1)	True	False
-logol			logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence								Up-to-date	http://logol.genouest.org/web/app.php/logol	Sequence Analysis		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	1.7.8	logol	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-peptimapper			peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag	Proteogenomics workflow for the expert annotation of eukaryotic genomes								To update	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9	Proteomics		genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	2.0			(0/4)	(0/4)	(0/4)	(0/4)	True	False
-GAFA			gafa	Gene Align and Family Aggregator								To update	http://aequatus.tgac.ac.uk	Visualization	gafa	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA	0.3.1			(0/1)	(0/1)	(1/1)	(0/1)	True	False
+PAMPA			pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2			(0/5)	(5/5)	(5/5)	(5/5)	True	True
 TreeBest			treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-blast_parser	296.0	27.0	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	blast_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	0.1.2			(0/1)	(0/1)	(1/1)	(0/1)	True	False
-ete	1255.0	67.0	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	(0/7)	(0/7)	(7/7)	(7/7)	True	True
-gblocks			gblocks	Gblocks								Up-to-date	http://molevol.cmima.csic.es/castresana/Gblocks.html	Sequence Analysis	gblocks	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	0.91b	gblocks	0.91b	(0/1)	(1/1)	(0/1)	(1/1)	True	False
-hcluster_sg	238.0	13.0	hcluster_sg	Hierarchically clustering on a sparse graph								To update	https://github.com/douglasgscofield/hcluster	Phylogenetics	hcluster_sg	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	0.5.1.1	hcluster_sg	0.5.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-hcluster_sg_parser	290.0	7.0	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	hcluster_sg_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	0.2.1			(0/1)	(0/1)	(1/1)	(0/1)	True	False
-lotus2	936.0	114.0	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	Up-to-date	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.32	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-miranda	6076.0	41.0	miranda	Finds potential target sites for miRNAs in genomic sequences								To update	http://www.microrna.org/	RNA	miranda	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	3.3a+galaxy1	miranda	3.3a	(0/1)	(0/1)	(1/1)	(1/1)	True	False
-smart_domains			smart_domains	SMART domains								To update	http://smart.embl.de/	Sequence Analysis	smart_domains	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	0.1.0	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-t_coffee	8690.0	70.0	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 abacas			abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23	(0/1)	(0/1)	(0/1)	(1/1)	True	True
-assemblystats			assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-bam2mappingstats			bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-bamclipper			bamclipper	Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.								Up-to-date	https://github.com/tommyau/bamclipper	Sequence Analysis	bamclipper	nml	https://github.com/tommyau/bamclipper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper	1.0.0	bamclipper	1.0.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-biohansel			biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-bundle_collections			bundle_collection	Tool to bundle up list collection into a single zip to be download								To update		Sequence Analysis	bundle_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections	1.3.0	perl-getopt-long	2.54	(0/1)	(1/1)	(0/1)	(1/1)	True	False
-collapse_collection			collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection								To update		Sequence Analysis	collapse_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection	5.1.0	gawk		(1/1)	(1/1)	(1/1)	(1/1)	True	False
-combineJSON			combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.								To update		Sequence Analysis	combine_json	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON	0.1			(0/1)	(0/1)	(0/1)	(0/1)	True	False
-combine_assembly_stats			combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.54	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-combine_tabular_collection			combine	Combine Tabular Collection into a single file								To update		Sequence Analysis	combine_tabular_collection	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection	0.1			(0/1)	(0/1)	(0/1)	(0/1)	True	False
-cryptogenotyper	8518.0	16.0	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-ectyper	9907.0	53.0	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-fasta2bed			fasta2bed	Convert multiple fasta file into tabular bed file format								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fasta2bed	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed	1.0.0	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-fasta_extract	10.0		fa-extract-sequence	extract single fasta from multiple fasta file								To update	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	Sequence Analysis	fasta_extract	nml	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract	1.1.0	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-fastqc_stats			FastQC_Summary	Summary multiple FastQC into a single tabular line report								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fastqc_stats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats	1.2	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-feht			feht	Automatically identify makers predictive of groups.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	feht	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht	0.1.0	feht	1.1.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-filter_spades_repeats			filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-getmlst			getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-hivtrace			hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-kaptive			kaptive	Kaptive reports information about capsular (K) loci found in genome assemblies.								To update		Sequence Analysis	kaptive	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive	0.3.0	kaptive	3.0.0b1	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-kat_filter			kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-mauve_contig_mover			mauve_contig_mover	Order a draft genome relative to a related reference genome								To update	https://github.com/phac-nml/mauve_contig_mover	Sequence Analysis	mauve_contig_mover	nml	https://github.com/phac-nml/mauve_contig_mover	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover	1.0.10	mauve	2.4.0.r4736	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-mob_suite	89021.0	322.0	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.8	(0/2)	(2/2)	(2/2)	(2/2)	True	True
-mrbayes			mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-mykrobe_parser			mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base		(0/1)	(0/1)	(0/1)	(0/1)	True	True
-pangolin	7276.0	259.0	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages								To update	https://github.com/hCoV-2019/pangolin	Sequence Analysis	pangolin	nml	https://github.com/hCoV-2019/pangolin	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin	1.1.14	pangolin	4.3	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-patrist			patrist	Extract Patristic Distance From a Tree								To update	https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02	Phylogenetics	patrist	nml	https://github.com/phac-nml/patrist	https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist	0.1.2	python		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-plasmid_profiler_suite				Plasmid Profiler suite defining all dependencies for Plasmid Profiler								To update		Sequence Analysis	suite_plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite				(0/1)	(0/1)	(0/1)	(0/1)	True	False
-plasmidspades			plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	3.15.5	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-promer			promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python		(0/1)	(0/1)	(0/1)	(0/1)	True	True
-pseudogenome			pseudogenome	Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	pseudogenome	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome	1.0.0	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-quasitools			aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality	A collection of tools for analysing Viral Quasispecies								Up-to-date	https://github.com/phac-nml/quasitools	Sequence Analysis	quasitools	nml	https://github.com/phac-nml/quasitools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools	0.7.0	quasitools	0.7.0	(0/12)	(12/12)	(0/12)	(12/12)	True	False
-refseq_masher			refseq_masher_contains, refseq_masher_matches	Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.								Up-to-date	https://github.com/phac-nml/refseq_masher	Sequence Analysis	refseq_masher	nml	https://github.com/phac-nml/refseq_masher	https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher	0.1.2	refseq_masher	0.1.2	(0/2)	(0/2)	(0/2)	(2/2)	True	False
-seqtk_nml			seqtk_nml_sample	Tool to downsample fastq reads								To update	https://github.com/lh3/seqtk	Sequence Analysis	seqtk_nml	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml	1.0.1	seqtk	1.4	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-sistr_cmd	2489.0	133.0	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2	(0/1)	(1/1)	(1/1)	(0/1)	True	True
-smalt			smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-spatyper			spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.								Up-to-date	https://github.com/HCGB-IGTP/spaTyper	Sequence Analysis	spatyper	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	0.3.3	spatyper	0.3.3	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-spolpred			spolpred	A program for predicting the spoligotype from raw sequence reads								To update		Sequence Analysis	spolpred	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred	1.0.1	spolpred		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-srst2	205.0	22.0	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-staramr	12673.0	889.0	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-stringmlst			stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-wade			wade	identify regions of interest								To update	https://github.com/phac-nml/wade	Sequence Analysis	wade	nml	https://github.com/phac-nml/wade	https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade	0.2.5+galaxy1	wade	0.2.6	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-isoplot	2.0	1.0	isoplot	Isoplot is a software for the visualisation of MS data from C13 labelling experiments								To update		Metabolomics, Visualization	isoplot	workflow4metabolomics	https://github.com/llegregam/Isoplot/tree/main	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot	1.3.0+galaxy1	isoplot	1.3.1	(0/1)	(0/1)	(1/1)	(1/1)	True	False
-repeatexplorer2			repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8			(0/1)	(0/1)	(1/1)	(0/1)	True	True
-ncbi_fcs_adaptor			ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.								To update	https://github.com/ncbi/fcs	Sequence Analysis	ncbi_fcs_adaptor	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	0.5.0			(1/1)	(0/1)	(0/1)	(0/1)	True	False
-suite_qiime2__alignment			qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
-suite_qiime2__composition			qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.2.0+q2galaxy.2024.2.1			(4/5)	(4/5)	(4/5)	(2/5)	True	True
-suite_qiime2__cutadapt			qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
-suite_qiime2__dada2			qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
-suite_qiime2__deblur			qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
-suite_qiime2__demux			qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.2.0+q2galaxy.2024.2.1			(6/9)	(6/9)	(6/9)	(6/9)	True	True
-suite_qiime2__diversity			qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.2.0+q2galaxy.2024.2.1			(21/22)	(21/22)	(21/22)	(21/22)	True	True
-suite_qiime2__diversity_lib			qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
-suite_qiime2__emperor			qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
-suite_qiime2__feature_classifier			qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.2.0+q2galaxy.2024.2.1			(10/11)	(10/11)	(10/11)	(10/11)	True	True
-suite_qiime2__feature_table			qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.2.2+q2galaxy.2024.2.1			(17/22)	(17/22)	(17/22)	(17/22)	True	True
-suite_qiime2__fragment_insertion			qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
-suite_qiime2__longitudinal			qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.2.0+q2galaxy.2024.2.1			(11/11)	(11/11)	(11/11)	(11/11)	True	True
-suite_qiime2__metadata			qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.2.0+q2galaxy.2024.2.1			(3/4)	(3/4)	(3/4)	(3/4)	True	True
-suite_qiime2__phylogeny			qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
-suite_qiime2__quality_control			qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.2.0+q2galaxy.2024.2.1			(6/10)	(6/10)	(6/10)	(6/10)	True	True
-suite_qiime2__quality_filter			qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.2.0+q2galaxy.2024.2.1			(1/1)	(1/1)	(1/1)	(1/1)	True	True
-suite_qiime2__rescript			qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.2.2+q2galaxy.2024.2.1			(0/25)	(0/25)	(0/25)	(0/25)	False	
-suite_qiime2__sample_classifier			qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.2.0+q2galaxy.2024.2.1			(15/15)	(15/15)	(15/15)	(15/15)	True	True
-suite_qiime2__taxa			qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
-suite_qiime2__vsearch			qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.2.0+q2galaxy.2024.2.1			(8/8)	(8/8)	(8/8)	(7/8)	True	True
-suite_qiime2_core__tools			qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.2.1+dist.he188c3c2			(2/3)	(2/3)	(2/3)	(2/3)	True	True
-suite_qiime2_core												To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core				(0/1)	(0/1)	(0/1)	(0/1)	True	True
-frogs			FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis								Up-to-date	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	4.1.0	(0/28)	(0/28)	(0/28)	(28/28)	True	True
-best_regression_subsets	3.0		BestSubsetsRegression1	Perform Best-subsets Regression								To update		Sequence Analysis, Variant Analysis	best_regression_subsets	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy		(1/1)	(0/1)	(1/1)	(1/1)	True	False
-blat_coverage_report			generate_coverage_report	Polymorphism of the Reads								To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0			(0/1)	(0/1)	(0/1)	(0/1)	True	False
-blat_mapping			blat2wig	Coverage of the Reads in wiggle format								To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0			(0/1)	(0/1)	(0/1)	(0/1)	True	False
-cd_hit_dup			cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1	(1/1)	(0/1)	(0/1)	(0/1)	True	True
-compute_motif_frequencies_for_all_motifs	94.0	2.0	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0			(0/1)	(1/1)	(1/1)	(0/1)	True	False
-compute_motifs_frequency	65.0		compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0			(0/1)	(1/1)	(1/1)	(0/1)	True	False
-count_gff_features	271.0	49.0	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-ctd_batch	203.0	13.0	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0			(0/1)	(0/1)	(1/1)	(0/1)	True	False
-cummerbund	1782.0	31.0	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem		(1/1)	(1/1)	(1/1)	(0/1)	True	False
-delete_overlapping_indels	39.0	2.0	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0			(0/1)	(0/1)	(1/1)	(0/1)	True	False
-divide_pg_snp	31.0		dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0			(1/1)	(0/1)	(1/1)	(0/1)	True	False
-express	325.0	12.0	express	Quantify the abundances of a set of target sequences from sampled subsequences								To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1	(0/1)	(1/1)	(1/1)	(0/1)	True	False
-featurecounter	22384.0	6.0	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.11.0	(1/1)	(0/1)	(1/1)	(0/1)	True	False
-filter_transcripts_via_tracking	20.0	1.0	filter_combined_via_tracking	Filter Combined Transcripts								To update		RNA	filter_transcripts_via_tracking	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1			(1/1)	(1/1)	(1/1)	(1/1)	True	False
-generate_pc_lda_matrix	119.0	12.0	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA								To update		Sequence Analysis	generate_pc_lda_matrix	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0			(1/1)	(1/1)	(1/1)	(1/1)	True	False
-getindelrates_3way			indelRates_3way	Estimate Indel Rates for 3-way alignments								To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.11.0	(1/1)	(0/1)	(0/1)	(0/1)	True	False
-getindels_2way			getIndels_2way	Fetch Indels from pairwise alignments								To update		Sequence Analysis, Variant Analysis	getindels_2way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy		(1/1)	(0/1)	(0/1)	(0/1)	True	False
-gmaj	11.0	4.0	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1			(1/1)	(1/1)	(1/1)	(1/1)	True	False
-hisat	228.0		hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-indels_3way	22.0		indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3			(1/1)	(0/1)	(1/1)	(0/1)	True	False
-logistic_regression_vif			LogisticRegression	Perform Logistic Regression with vif								To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-maf_cpg_filter			cpgFilter	Mask CpG/non-CpG sites from MAF file								To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.11.0	(1/1)	(0/1)	(0/1)	(0/1)	True	False
-mapping_to_ucsc			mapToUCSC	Format mapping data as UCSC custom track								To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0			(0/1)	(0/1)	(0/1)	(0/1)	True	False
-microsatellite_birthdeath			microsatellite_birthdeath	Identify microsatellite births and deaths								To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0			(0/1)	(0/1)	(0/1)	(0/1)	True	False
-microsats_alignment_level			microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments								To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik		(1/1)	(0/1)	(0/1)	(0/1)	True	False
-microsats_mutability			microsats_mutability1	Estimate microsatellite mutability by specified attributes								To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.11.0	(1/1)	(0/1)	(0/1)	(0/1)	True	False
-multispecies_orthologous_microsats			multispecies_orthologous_microsats	Extract orthologous microsatellites								To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-quality_filter			qualityFilter	Filter nucleotides based on quality scores								To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.11.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-rcve			rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R		(1/1)	(0/1)	(0/1)	(0/1)	True	False
-short_reads_figure_high_quality_length			hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-short_reads_figure_score	163.0	13.0	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig		(0/1)	(0/1)	(1/1)	(0/1)	True	False
-substitution_rates			subRate1	Estimate substitution rates for non-coding regions								To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0			(0/1)	(0/1)	(0/1)	(0/1)	True	False
-substitutions			substitutions1	Fetch substitutions from pairwise alignments								To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.11.0	(1/1)	(0/1)	(0/1)	(0/1)	True	False
-tophat	1.0		tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.20	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-tophat2	24167.0	312.0	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.3	(1/1)	(1/1)	(1/1)	(0/1)	True	False
-ucsc_custom_track	393.0	45.0	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python		(1/1)	(0/1)	(1/1)	(0/1)	True	False
-weightedaverage			wtavg	Assign weighted-average of the values of features overlapping an interval								To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0	(1/1)	(0/1)	(0/1)	(0/1)	True	False
-windowsplitter			winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.11.0	(1/1)	(0/1)	(0/1)	(0/1)	True	False
-hgv_fundo			hgv_funDo	FunDO human genes associated with disease terms								To update		Sequence Analysis	hgv_fundo	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0			(1/1)	(0/1)	(1/1)	(0/1)	True	False
-hgv_hilbertvis			hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve								To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R		(1/1)	(0/1)	(1/1)	(0/1)	True	False
-find_diag_hits	69.0	5.0	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-gi2taxonomy	660.0	27.0	Fetch Taxonomic Ranks	Fetch taxonomic representation								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-kraken2tax	14683.0	481.0	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk		(1/1)	(1/1)	(1/1)	(0/1)	True	True
-lca_wrapper	137.0	2.0	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-poisson2test	116.0	6.0	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0	(0/1)	(1/1)	(1/1)	(0/1)	True	False
-t2ps	457.0	31.0	Draw_phylogram	Draw phylogeny								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-t2t_report	947.0	26.0	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-AggregateAlignments			graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-AlignCluster			graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-CMFinder			cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-CollectResults			glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-CollectResultsNoAlign			graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-GSPAN			gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-LocARNAGraphClust			locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-NSPDK			NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0	(0/2)	(0/2)	(2/2)	(0/2)	True	False
-Plotting			motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn		(0/1)	(0/1)	(1/1)	(0/1)	True	False
-PrepareForMlocarna			preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-Preprocessing			preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-Structure_GSPAN			structure_to_gspan	Convert RNA structure to GSPAN graphs								To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-antismash	14596.0	279.0	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	(1/1)	(1/1)	(1/1)	(0/1)	True	True
-augustus	8864.0	516.0	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.								To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-bamhash	169.0	15.0	bamhash	Hash BAM and FASTQ files to verify data integrity								Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-barcode_collapse			barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-bionano			bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0			(1/1)	(1/1)	(1/1)	(0/1)	True	False
-bismark	13575.0	404.0	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2	(0/4)	(4/4)	(4/4)	(4/4)	True	False
-blobtoolkit	685.0	21.0	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7			(0/1)	(1/1)	(1/1)	(0/1)	True	False
-blockbuster	3009.0	34.0	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1	(1/1)	(1/1)	(1/1)	(0/1)	True	False
-chipseeker	15690.0	418.0	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0	(1/1)	(1/1)	(1/1)	(0/1)	True	False
-circexplorer	251.0	8.0	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10	(0/1)	(1/1)	(1/1)	(0/1)	True	False
-combine_metaphlan_humann			combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		(0/1)	(0/1)	(1/1)	(0/1)	True	True
-compare_humann2_output	332.0	10.0	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			(0/1)	(0/1)	(0/1)	(0/1)	True	True
-crt			crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-flye	20904.0	1499.0	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.3	flye	2.9.3	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-format_metaphlan2_output	5588.0	166.0	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			(0/1)	(0/1)	(1/1)	(0/1)	True	True
-gfastats	8159.0	418.0	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	Up-to-date	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.6	(1/1)	(1/1)	(1/1)	(0/1)	True	False
-glimmer_hmm				GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm				(0/1)	(0/1)	(0/1)	(0/1)	True	True
-gotohscan	71.0	1.0	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-graphclust	6.0		graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-graphmap			graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.3	(0/2)	(0/2)	(2/2)	(0/2)	True	True
-hifiasm	1410.0	297.0	hifiasm	A fast haplotype-resolved de novo assembler								To update	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	0.19.8	hifiasm	0.19.9	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-homer				Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer				(0/1)	(0/1)	(0/1)	(0/1)	True	False
-illumina_methylation_analyser			illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-instagraal	139.0	14.0	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			(0/1)	(0/1)	(1/1)	(0/1)	True	False
-iprscan5				Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5				(0/1)	(0/1)	(0/1)	(0/1)	True	True
-itsx	868.0	38.0	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-labels			bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-lighter	152.0	9.0	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-mafft	143045.0	817.0	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.520	mafft	7.525	(2/2)	(2/2)	(2/2)	(2/2)	True	True
-methtools			methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools		(0/8)	(0/8)	(0/8)	(0/8)	True	False
-methyldackel			pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1	(1/1)	(1/1)	(1/1)	(0/1)	True	False
-metilene	3966.0	103.0	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-miclip			mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-minced	895.0	53.0	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-minipolish	185.0	21.0	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-mitohifi	613.0	56.0	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3			(1/1)	(1/1)	(1/1)	(0/1)	True	False
-nextdenovo	268.0	84.0	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-nucleosome_prediction	861.0	2.0	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-openms			AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.1.0	(7/140)	(34/140)	(135/140)	(0/140)	True	False
-peakachu	3109.0	78.0	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-pfamscan	165.0	19.0	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-piranha	1809.0	39.0	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-platypus			bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-plotly_ml_performance_plots	1323.0	71.0	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.3	galaxy-ml	0.10.0	(1/1)	(1/1)	(1/1)	(0/1)	True	False
-plotly_parallel_coordinates_plot	652.0	37.0	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python		(1/1)	(1/1)	(1/1)	(0/1)	True	False
-plotly_regression_performance_plots	843.0	79.0	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python		(1/1)	(1/1)	(1/1)	(0/1)	True	False
-protease_prediction	149.0	4.0	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-protein_properties	256.0	15.0	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-improviser			proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1			(0/1)	(0/1)	(0/1)	(0/1)	True	False
-racon	21353.0	309.0	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-repeat_masker	3750.0	248.0	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.1.5	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-antarna	52.0	2.0	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-aresite2	65.0	4.0	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python		(0/1)	(0/1)	(1/1)	(0/1)	True	False
-blockclust	1478.0	15.0	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1	(1/1)	(1/1)	(1/1)	(0/1)	True	False
-cmsearch_deoverlap	102.0	1.0	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		(0/1)	(0/1)	(1/1)	(0/1)	True	True
-cmv	70.0	1.0	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8	(0/4)	(0/4)	(2/4)	(0/4)	True	False
-cofold	342.0	8.0	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-compalignp	220.0		compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-coprarna			coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-dewseq	72.0	11.0	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python		(0/1)	(0/1)	(1/1)	(0/1)	True	False
-dorina	1086.0	1.0	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0			(0/1)	(0/1)	(1/1)	(0/1)	True	False
-dot2ct			rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-dotknot	83.0	1.0	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna		(0/1)	(0/1)	(1/1)	(0/1)	True	False
-exparna			exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.								Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-graphprot			graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.								To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy1	graphprot	1.1.7	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-htseq-clip			htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets								To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-infernal	100230.0	67.0	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	(0/6)	(6/6)	(6/6)	(0/6)	True	True
-inforna				INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.								To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna				(0/1)	(0/1)	(0/1)	(0/1)	True	False
-intarna	7569.0	23.0	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.								Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.0	intarna	3.4.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-kinwalker	70.0	3.0		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.								To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker				(0/1)	(0/1)	(0/1)	(0/1)	True	False
-locarna			locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								To update	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	1.9.2.3	locarna	2.0.0	(0/5)	(0/5)	(1/5)	(0/5)	True	False
-mea	85.0	3.0	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-mqc	76.0	5.0	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-nastiseq	40.0		nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-paralyzer	299.0	7.0	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-pipmir	275.0	21.0	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-rRNA			meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0		(0/1)	(0/1)	(0/1)	(0/1)	True	True
-rbpbench	36.0		rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	Up-to-date	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	0.8.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-rcas	1226.0	38.0	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-reago			reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-remurna	42.0	2.0	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-ribotaper	628.0	44.0	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	(0/3)	(0/3)	(3/3)	(0/3)	True	False
-rna_shapes			RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@		(0/1)	(0/1)	(1/1)	(0/1)	True	False
-rnabob	164.0	3.0	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-rnacode	1358.0	5.0	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-rnacommender	1074.0	6.0	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-rnalien	33.0	4.0	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-rnasnp	86.0	5.0	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-rnaz	42965.0	14.0	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1	(0/6)	(0/6)	(6/6)	(0/6)	True	False
-selectsequencesfrommsa	457.0	27.0	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-sortmerna	18504.0	376.0	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	Up-to-date	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.6	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-sshmm	223.0	5.0	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-targetfinder	713.0	37.0	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7	(1/1)	(1/1)	(1/1)	(0/1)	True	False
-trna_prediction	2935.0	236.0	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41	(0/2)	(2/2)	(2/2)	(0/2)	True	False
-vienna_rna	799.0		viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4	(0/23)	(0/23)	(21/23)	(0/23)	True	False
-sailfish	4024.0	55.0	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2		(1/1)	(1/1)	(1/1)	(1/1)	True	False
-salmon	55161.0	746.0	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	(2/3)	(1/3)	(3/3)	(1/3)	True	True
-tapscan			tapscan_classify	Search for transcription associated proteins (TAPs)								To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-tgsgapcloser	460.0	36.0	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-trim_galore	238699.0	2334.0	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-uniprot_rest_interface	2406.0	132.0	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.4	requests		(1/1)	(1/1)	(1/1)	(0/1)	True	False
-vt			vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-wtdbg	1660.0	116.0	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	(0/1)	(0/1)	(1/1)	(1/1)	True	True
-align_back_trans	329.0	11.0	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-chromosome_diagram			chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-clc_assembly_cell			clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.20	(0/2)	(0/2)	(0/2)	(0/2)	True	False
-clinod			clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	(1/1)	(0/1)	(0/1)	(0/1)	True	True
-count_roi_variants			count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.20	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-coverage_stats			coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.20	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-effectiveT3			effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-fasta_filter_by_id			fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-fastq_filter_by_id			fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-fastq_pair_names			fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.1.5	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-fastq_paired_unpaired			fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.1.5	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-get_orfs_or_cdss	7.0		get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70	(0/1)	(1/1)	(1/1)	(1/1)	True	False
-mummer	652.0	83.0	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18	(1/1)	(0/1)	(1/1)	(0/1)	True	False
-nlstradamus			nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-predictnls			predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10			(0/1)	(0/1)	(0/1)	(0/1)	True	False
-protein_analysis			promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter		(0/6)	(0/6)	(6/6)	(0/6)	True	False
-sample_seqs	3765.0	149.0	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-samtools_depad			samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.20	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-samtools_depth	4948.0	296.0	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.20	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-samtools_idxstats	48426.0	1450.0	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.20	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-seq_composition	874.0	71.0	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70	(1/1)	(0/1)	(1/1)	(1/1)	True	False
-seq_filter_by_id	25302.0	306.0	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-seq_filter_by_mapping	3784.0	82.0	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-seq_length			seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-seq_primer_clip			seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-seq_rename			seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-seq_select_by_id			seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70	(0/1)	(1/1)	(0/1)	(0/1)	True	False
-venn_list	5067.0	248.0	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.1.5	(1/1)	(0/1)	(1/1)	(1/1)	True	False
-suite_qiime2__alignment			qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
-suite_qiime2__composition			qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.2.0+q2galaxy.2024.2.1			(4/5)	(4/5)	(4/5)	(2/5)	True	True
-suite_qiime2__cutadapt			qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
-suite_qiime2__dada2			qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
-suite_qiime2__deblur			qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
-suite_qiime2__demux			qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.2.0+q2galaxy.2024.2.1			(6/9)	(6/9)	(6/9)	(6/9)	True	True
-suite_qiime2__diversity			qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.2.0+q2galaxy.2024.2.1			(21/22)	(21/22)	(21/22)	(21/22)	True	True
-suite_qiime2__diversity_lib			qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
-suite_qiime2__emperor			qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
-suite_qiime2__feature_classifier			qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.2.0+q2galaxy.2024.2.1			(10/11)	(10/11)	(10/11)	(10/11)	True	True
-suite_qiime2__feature_table			qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.2.2+q2galaxy.2024.2.1			(17/22)	(17/22)	(17/22)	(17/22)	True	True
-suite_qiime2__fragment_insertion			qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
-suite_qiime2__longitudinal			qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.2.0+q2galaxy.2024.2.1			(11/11)	(11/11)	(11/11)	(11/11)	True	True
-suite_qiime2__metadata			qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.2.0+q2galaxy.2024.2.1			(3/4)	(3/4)	(3/4)	(3/4)	True	True
-suite_qiime2__phylogeny			qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
-suite_qiime2__quality_control			qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.2.0+q2galaxy.2024.2.1			(6/10)	(6/10)	(6/10)	(6/10)	True	True
-suite_qiime2__quality_filter			qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.2.0+q2galaxy.2024.2.1			(1/1)	(1/1)	(1/1)	(1/1)	True	True
-suite_qiime2__rescript			qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.2.2+q2galaxy.2024.2.1			(0/25)	(0/25)	(0/25)	(0/25)	False	
-suite_qiime2__sample_classifier			qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.2.0+q2galaxy.2024.2.1			(15/15)	(15/15)	(15/15)	(15/15)	True	True
-suite_qiime2__taxa			qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
-suite_qiime2__vsearch			qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.2.0+q2galaxy.2024.2.1			(8/8)	(8/8)	(8/8)	(7/8)	True	True
-suite_qiime2_core__tools			qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.2.1+dist.he188c3c2			(2/3)	(2/3)	(2/3)	(2/3)	True	True
-suite_qiime2_core												To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core				(0/1)	(0/1)	(0/1)	(0/1)	True	True
-frogs			FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis								Up-to-date	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	4.1.0	(0/28)	(0/28)	(0/28)	(28/28)	True	True
-TrimNs			trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
 abricate	496717.0	1764.0	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	(3/3)	(3/3)	(3/3)	(3/3)	True	True
 abritamr			abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	To update	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.14	abritamr	1.0.17	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 abyss	4278.0	391.0	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.7	abyss	2.3.7	(0/1)	(1/1)	(1/1)	(0/1)	True	True
-adapter_removal	217.0	37.0	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.3	adapterremoval	2.3.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-aegean			aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	(1/4)	(4/4)	(4/4)	(4/4)	True	False
 aldex2	129.0	13.0	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 amplican	53.0	12.0	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-ampvis2			ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn	ampvis2	ampvis	ampvis		ampvis	ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.	Analysis, Visualisation	Biodiversity	To update	https://github.com/MadsAlbertsen/ampvis2/	Metagenomics	ampvis2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2	2.8.6			(0/19)	(0/19)	(19/19)	(0/19)	True	False
 amrfinderplus	591.0		amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	To update	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.11.26	ncbi-amrfinderplus	3.12.8	(0/1)	(0/1)	(1/1)	(1/1)	True	True
 ancombc	7.0	4.0	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-anndata			anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Transcriptomics, Sequence Analysis	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.3	anndata	0.6.22.post1	(5/5)	(4/5)	(5/5)	(0/5)	True	False
-annotatemyids	26115.0	1175.0	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-arriba	3436.0	28.0	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0	(0/3)	(3/3)	(3/3)	(0/3)	True	False
-art			art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	art	art		ART	ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD	Conversion	Bioinformatics	To update		Sequence Analysis, Data Source	art	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/art	https://github.com/galaxyproject/tools-iuc/tree/main/tools/art	2014.11.03.0	art	2016.06.05	(0/3)	(0/3)	(0/3)	(0/3)	True	False
+antismash	14596.0	279.0	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	(1/1)	(1/1)	(1/1)	(0/1)	True	True
 artic			artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	(0/2)	(0/2)	(2/2)	(0/2)	True	True
-assembly-stats			assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02	(0/1)	(0/1)	(0/1)	(1/1)	True	False
-augustus	8864.0	516.0	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	augustus	augustus		AUGUSTUS	AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.	Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus	3.4.0	augustus	3.5.0	(2/2)	(2/2)	(2/2)	(2/2)	True	False
-b2btools			b2btools_single_sequence	This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.	b2btools	b2btools		b2bTools	The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA	Protein disorder prediction, Protein secondary structure prediction, Protein feature detection		To update	https://bio2byte.be	Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools	3.0.5+galaxy0	b2btools	3.0.6	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+assemblystats			assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	True
 bakta	2982.0	151.0	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	Bakta	Bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	To update	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.2	bakta	1.9.3	(0/1)	(1/1)	(1/1)	(1/1)	True	True
-bamutil			bamutil_clip_overlap, bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.								To update	https://github.com/statgen/bamUtil	Sequence Analysis	bamutil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil		bamutil	1.0.15	(1/2)	(1/2)	(1/2)	(0/2)	True	False
+bamtools	14039.0	208.0	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	(1/1)	(0/1)	(1/1)	(1/1)	True	True
 bandage	44390.0	2016.0	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	(2/2)	(2/2)	(2/2)	(2/2)	True	True
-baredsc			baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	(4/4)	(0/4)	(4/4)	(0/4)	True	False
-barrnap	3938.0	160.0	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	barrnap	barrnap		Barrnap	Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).	Gene prediction	Genomics, Model organisms, Model organisms	To update		Sequence Analysis	barrnap	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap	1.2.2	barrnap	0.9	(0/1)	(1/1)	(1/1)	(1/1)	True	False
-bax2bam	200.0	8.0	bax2bam	BAX to BAM converter								Up-to-date	https://github.com/pacificbiosciences/bax2bam/	Convert Formats, Sequence Analysis	bax2bam	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam	0.0.11	bax2bam	0.0.11	(1/1)	(0/1)	(1/1)	(0/1)	True	False
 bayescan	64.0	8.0	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 bbtools			bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.								Up-to-date	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.06	bbmap	39.06	(6/6)	(1/6)	(5/6)	(0/6)	True	True
-bctools			bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2	(0/7)	(0/7)	(7/7)	(0/7)	True	False
-bellerophon	1194.0	123.0	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.								Up-to-date	https://github.com/davebx/bellerophon	Sequence Analysis	bellerophon	iuc	https://github.com/davebx/bellerophon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon	1.0	bellerophon	1.0	(1/1)	(1/1)	(1/1)	(0/1)	True	False
 bigscape			bigscape	Construct sequence similarity networks of BGCs and groups them into GCF								Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 binning_refiner	81.0	21.0	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-bioinformatics_cafe			fasta_regex_finder	Miscellanea of scripts for bioinformatics								To update	https://github.com/dariober/bioinformatics-cafe/	Sequence Analysis	bioinformatics_cafe	mbernt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe	0.1.0	python		(1/1)	(0/1)	(1/1)	(0/1)	True	False
+biohansel			biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1	(0/1)	(0/1)	(0/1)	(0/1)	True	True
 biom_format			biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	(2/6)	(2/6)	(6/6)	(0/6)	True	True
-bioperl			bp_genbank2gff3	Converts GenBank format files to GFF3	bioperl	bioperl		BioPerl	A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.	Data handling, Service invocation	Genomics, Software engineering, Data management	To update	https://bioperl.org/	Sequence Analysis	bp_genbank2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl	1.1	perl-bioperl	1.7.8	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-biscot	3.0	1.0	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-blastxml_to_gapped_gff3	185.0	24.0	blastxml_to_gapped_gff3	BlastXML to gapped GFF3								To update		Convert Formats, Sequence Analysis	blastxml_to_gapped_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3	1.1	bcbiogff	0.6.6	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+biotradis			bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	(3/3)	(0/3)	(0/3)	(0/3)	True	True
+blast2go	1232.0	101.0	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe		(0/1)	(0/1)	(0/1)	(0/1)	True	True
+blast_rbh	22499.0	121.0	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+blastxml_to_top_descr	264558.0	159.0	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python		(0/1)	(0/1)	(1/1)	(0/1)	True	True
 bracken	18351.0	326.0	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	2.9	bracken	2.9	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 busco	86180.0	1804.0	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	To update	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.5.0	busco	5.7.1	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-bwameth	10619.0	201.0	bwameth	Fast and accurate alignment of BS-seq reads								To update	https://github.com/brentp/bwa-meth	Sequence Analysis, Next Gen Mappers	bwameth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth	0.2.6	bwameth	0.2.7	(1/1)	(1/1)	(1/1)	(0/1)	True	False
-cactus			cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	cactus		Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			(0/2)	(2/2)	(2/2)	(1/2)	True	False
-calculate_contrast_threshold			calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.								To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold	1.0.0	numpy		(0/1)	(0/1)	(0/1)	(0/1)	True	False
 cat			cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	(5/5)	(2/5)	(5/5)	(0/5)	True	True
+cd_hit_dup			cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1	(1/1)	(0/1)	(0/1)	(0/1)	True	True
 cdhit	8278.0	6.0	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	(0/1)	(0/1)	(1/1)	(1/1)	True	True
 cemitool	98.0	9.0	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	To update	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.18.1	bioconductor-cemitool	1.26.0	(1/1)	(0/1)	(1/1)	(0/1)	True	True
-charts	3589.0	287.0	charts	Enables advanced visualization options in Galaxy Charts								To update		Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts	1.0.1	r-getopt		(0/1)	(0/1)	(0/1)	(0/1)	True	False
 checkm			checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	To update	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.0	checkm-genome	1.2.2	(0/10)	(0/10)	(10/10)	(10/10)	True	True
-cherri			cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8	(0/2)	(0/2)	(2/2)	(0/2)	True	False
-chira	74.0		chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3	(5/5)	(0/5)	(5/5)	(0/5)	True	False
-chromeister	2130.0	182.0	chromeister	ultra-fast pairwise genome comparisons								Up-to-date	https://github.com/estebanpw/chromeister	Sequence Analysis	chromeister	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister	1.5.a	chromeister	1.5.a	(0/1)	(1/1)	(1/1)	(1/1)	True	False
-circexplorer2	269.0	16.0	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8	(0/1)	(0/1)	(1/1)	(0/1)	True	False
 clair3	1856.0	68.0	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	0.1.12	clair3	1.0.8	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+clinod			clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	(1/1)	(0/1)	(0/1)	(0/1)	True	True
 clustalw	46793.0	651.0	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+cmsearch_deoverlap	102.0	1.0	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		(0/1)	(0/1)	(1/1)	(0/1)	True	True
 codeml	60901.0	29.0	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 cojac			cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.1	cojac	0.9.1	(2/3)	(0/3)	(3/3)	(0/3)	True	True
-colabfold			colabfold_alphafold, colabfold_msa	Protein prediction based on AlphaFold2	Colabfold	Colabfold		ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.	Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	To update	https://github.com/sokrypton/ColabFold	Proteomics, Graphics	colabfold	iuc	https://github.com/sokrypton/ColabFold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold	1.5.5			(2/2)	(0/2)	(0/2)	(0/2)	True	False
-colibread			commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak	Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome								To update	https://colibread.inria.fr/	Sequence Analysis, Variant Analysis	colibread	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread	24.7.14+galaxy0	commet	24.7.14	(0/7)	(0/7)	(1/7)	(1/7)	True	False
+combine_assembly_stats			combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.54	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+combine_metaphlan_humann			combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		(0/1)	(0/1)	(1/1)	(0/1)	True	True
+compare_humann2_output	332.0	10.0	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			(0/1)	(0/1)	(0/1)	(0/1)	True	True
 compleasm			compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	(0/1)	(0/1)	(1/1)	(1/1)	True	True
 concoct	250.0	29.0	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	(0/5)	(0/5)	(5/5)	(5/5)	True	True
-coverage_report			CoverageReport2	Generate Detailed Coverage Report from BAM file								To update	https://github.com/galaxyproject/tools-iuc	Sequence Analysis	coverage_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report	0.0.4	perl-number-format	1.76	(0/1)	(0/1)	(0/1)	(0/1)	True	False
 coverm			coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	(0/2)	(0/2)	(2/2)	(2/2)	True	True
-crispr_studio	636.0	30.0	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	crisprstudio	crisprstudio		CRISPRStudio	CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.	Visualisation	Sequence analysis, Genomics, Data visualisation	To update	https://github.com/moineaulab/CRISPRStudio	Sequence Analysis	crispr_studio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio	1+galaxy0	crispr_studio	1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-crosscontamination_barcode_filter	347.0	17.0	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+cryptogenotyper	8518.0	16.0	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 cutadapt	232004.0	5090.0	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.8	cutadapt	4.8	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 dada2			dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	(10/10)	(10/10)	(10/10)	(10/10)	True	True
 das_tool	550.0	17.0	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	(0/2)	(0/2)	(2/2)	(2/2)	True	True
-deepsig	5.0		deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5	(0/1)	(0/1)	(1/1)	(1/1)	True	False
 deseq2	95752.0	4990.0	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-dexseq	16064.0	218.0	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	(3/3)	(3/3)	(3/3)	(3/3)	True	False
 diamond	49711.0	963.0	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	(3/3)	(3/3)	(3/3)	(3/3)	True	True
 disco	369.0	42.0	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	(1/1)	(0/1)	(1/1)	(0/1)	True	True
 dram			dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	To update	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.3.5	dram	1.5.0	(0/5)	(0/5)	(5/5)	(0/5)	True	True
 drep			drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	To update	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.4.5	drep	3.5.0	(0/2)	(0/2)	(2/2)	(2/2)	True	True
-dropletutils	3934.0	126.0	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Transcriptomics, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0	(1/1)	(1/1)	(1/1)	(0/1)	True	False
-edger	18522.0	945.0	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-egsea	2524.0	177.0	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+ectyper	9907.0	53.0	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+effectiveT3			effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+eggnog_mapper	30565.0	510.0	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	(3/3)	(3/3)	(3/3)	(3/3)	True	True
 emboss_5	89530.0	1816.0	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	(107/107)	(107/107)	(107/107)	(107/107)	True	True
-exomedepth	410.0	29.0	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	exomedepth	exomedepth		ExomeDepth	Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	(1/1)	(0/1)	(1/1)	(0/1)	True	False
-exonerate	988.0	59.0	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	exonerate	exonerate		Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate	2.4.0	exonerate	2.4.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+ete	1255.0	67.0	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	(0/7)	(0/7)	(7/7)	(7/7)	True	True
 export2graphlan	5265.0	200.0	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+ez_histograms			ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1	(0/1)	(0/1)	(0/1)	(0/1)	True	True
 fargene	459.0	52.0	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	(1/1)	(0/1)	(1/1)	(0/1)	True	True
-fasta_nucleotide_color_plot	322.0	39.0	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot	1.0.1	openjdk		(1/1)	(0/1)	(1/1)	(0/1)	True	False
-fasta_stats	35332.0	1080.0	fasta-stats	Display summary statistics for a fasta file.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats	2.0	numpy		(1/1)	(1/1)	(1/1)	(1/1)	True	False
 fastani	3498.0	250.0	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity								To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	(0/1)	(0/1)	(1/1)	(1/1)	True	True
-fastk			fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0	(0/1)	(0/1)	(1/1)	(0/1)	False	
+fastk			fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 fastp	1055760.0	2803.0	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 fastqe	4333.0	1266.0	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 fasttree	55434.0	379.0	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 featurecounts	696399.0	4679.0	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-feelnc	1191.0	46.0	feelnc	Galaxy wrapper for FEELnc	feelnc	feelnc		FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.	Annotation, Classification	RNA-seq, Functional, regulatory and non-coding RNA	To update	https://github.com/tderrien/FEELnc	Sequence Analysis	feelnc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc	0.2.1	feelnc	0.2	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-fermikit			fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193	(0/2)	(0/2)	(0/2)	(0/2)	True	False
-fgsea	5240.0	307.0	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+filter_spades_repeats			filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	True
 filtlong	30483.0	617.0	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-flair			flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0	(0/2)	(0/2)	(2/2)	(0/2)	True	False
-flash	13759.0	74.0	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+flashlfq	645.0	17.0	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	(0/1)	(1/1)	(1/1)	(0/1)	True	True
+flye	20904.0	1499.0	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.3	flye	2.9.3	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+format_metaphlan2_output	5588.0	166.0	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			(0/1)	(0/1)	(1/1)	(0/1)	True	True
 fraggenescan	1102.0	68.0	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	(0/1)	(1/1)	(1/1)	(1/1)	True	True
 freyja			freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja						To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.0	(2/4)	(0/4)	(4/4)	(0/4)	True	True
+frogs			FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis								Up-to-date	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	4.1.0	(0/28)	(0/28)	(0/28)	(28/28)	True	True
+frogs			FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis								Up-to-date	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	4.1.0	(0/28)	(0/28)	(0/28)	(28/28)	True	True
+frogs			FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis								Up-to-date	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	4.1.0	(0/28)	(0/28)	(0/28)	(28/28)	True	True
+frogs			FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis								Up-to-date	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	4.1.0	(0/28)	(0/28)	(0/28)	(28/28)	True	True
 funannotate			funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			(3/5)	(5/5)	(5/5)	(5/5)	True	True
-gecko	519.0	112.0	gecko	Ungapped genome comparison								Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko	1.2	gecko	1.2	(0/1)	(1/1)	(1/1)	(0/1)	True	False
-gemini	1209.0		gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini	0.20.1	gemini	0.30.2	(1/3)	(2/3)	(2/3)	(2/3)	True	False
-geneiobio	44.0	3.0	gene_iobio_display_generation_iframe	Gene.iobio is an interactive tool for variant and trio analysis.								To update	https://github.com/iobio/gene.iobio	Sequence Analysis	geneiobio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio	4.7.1+galaxy1			(0/1)	(1/1)	(1/1)	(0/1)	True	False
-genomic_super_signature	46.0	11.0	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-getorganelle	495.0	18.0	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	(0/2)	(2/2)	(2/2)	(0/2)	True	False
-gff3_rebase	110.0	12.0	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	Sequence Analysis	gff3_rebase	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase	1.2	bcbiogff	0.6.6	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-gffread	10995.0	680.0	gffread	gffread filters and/or converts GFF3/GTF2 records	gffread	gffread		gffread	program for filtering, converting and manipulating GFF files	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/	Sequence Analysis	gffread	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread	0.12.7	gffread	0.12.7	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+getmlst			getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0	(0/1)	(0/1)	(0/1)	(0/1)	True	True
 ggplot2			ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		(5/5)	(5/5)	(5/5)	(5/5)	True	True
+gi2taxonomy	660.0	27.0	Fetch Taxonomic Ranks	Fetch taxonomic representation								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 glimmer			glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	(0/8)	(0/8)	(4/8)	(0/8)	True	True
+glimmer_hmm				GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm				(0/1)	(0/1)	(0/1)	(0/1)	True	True
 goenrichment	5206.0	321.0	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de CiĂŞncia.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	(2/2)	(2/2)	(2/2)	(2/2)	True	True
 goseq	19167.0	1210.0	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 graphlan	5002.0	247.0	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	(2/2)	(2/2)	(2/2)	(2/2)	True	True
+graphmap			graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.3	(0/2)	(0/2)	(2/2)	(0/2)	True	True
 gtdbtk			gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	To update	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.3.2	gtdbtk	2.4.0	(0/1)	(1/1)	(1/1)	(0/1)	True	True
 gubbins	3340.0	145.0	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	(1/1)	(1/1)	(1/1)	(0/1)	True	True
-gwastools			gwastools_manhattan_plot		gwastools	gwastools		GWASTools	Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.	Deposition, Analysis, Annotation	GWAS study	To update	https://bioconductor.org/packages/release/bioc/html/GWASTools.html	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools	0.1.0	bioconductor-gwastools	1.48.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
 hamronization			hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	(0/2)	(0/2)	(2/2)	(2/2)	True	True
 hansel			bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	(1/1)	(0/1)	(1/1)	(0/1)	True	True
-hapcut2			hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	(0/1)	(1/1)	(0/1)	(0/1)	True	False
-hapog	295.0	36.0	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	(0/1)	(0/1)	(1/1)	(1/1)	True	False
-heatmap2			ggplot2_heatmap2	heatmap.2 function from the R gplots package								To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2	3.1.3.1	r-gplots	2.17.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-heinz	1186.0	242.0	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	bionet, heinz		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	(4/4)	(4/4)	(4/4)	(0/4)	True	False
-hicexplorer			hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictadclassifier, hicexplorer_hictraintadclassifier, hicexplorer_hictransform, hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.								To update	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer	3.7.2	hicexplorer	3.7.4	(0/40)	(5/40)	(40/40)	(4/40)	True	False
-hicstuff			hicstuff_pipeline									To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff	3.1.5	hicstuff	3.2.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
 hifiasm_meta	137.0	12.0	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	(0/1)	(1/1)	(1/1)	(0/1)	True	True
-hisat2	299104.0	4183.0	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+hivtrace			hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0	(0/1)	(0/1)	(0/1)	(0/1)	True	True
 hmmer3	21049.0	111.0	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	(0/12)	(12/12)	(12/12)	(12/12)	True	True
-homer			homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide	HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.	homer	homer		homer	HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.	Sequence motif discovery		Up-to-date	http://homer.ucsd.edu/homer/index.html	Sequence Analysis	data_manager_homer_preparse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer	4.11	homer	4.11	(0/5)	(0/5)	(5/5)	(4/5)	True	False
-htseq_count	154533.0	1419.0	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	htseq	htseq		HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data	Nucleic acid sequence analysis	Sequence analysis	Up-to-date	https://readthedocs.org/projects/htseq/	Genomic Interval Operations, SAM, Sequence Analysis, RNA	htseq_count	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count	2.0.5	htseq	2.0.5	(1/1)	(1/1)	(1/1)	(1/1)	True	False
 humann	5856.0	247.0	humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	Up-to-date	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.8	humann	3.8	(6/13)	(12/13)	(13/13)	(13/13)	True	True
-hybpiper			hybpiper	Analyse targeted sequence capture data	HybPiper	HybPiper		HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	To update	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper	2.1.6	hybpiper	2.1.7	(0/1)	(1/1)	(1/1)	(0/1)	True	False
 hyphy			hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.61	(17/17)	(2/17)	(17/17)	(2/17)	True	True
 hypo	354.0	39.0	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 icescreen			icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	(0/1)	(0/1)	(0/1)	(0/1)	True	True
 idba_ud	721.0	43.0	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	(3/3)	(0/3)	(3/3)	(3/3)	True	True
-idr	2873.0	30.0	idr	Galaxy wrappers for the IDR package from Nathan Boleu								To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr	2.0.3	idr	2.0.4.2	(1/1)	(0/1)	(1/1)	(0/1)	True	False
-iedb_api	1506.0	12.0	iedb_api	Get epitope binding predictions from IEDB-API								To update	http://tools.immuneepitope.org/main/tools-api/	Data Source, Sequence Analysis	iedb_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api	2.15.2	python		(0/1)	(0/1)	(1/1)	(0/1)	True	False
+infernal	100230.0	67.0	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	(0/6)	(6/6)	(6/6)	(0/6)	True	True
 instrain			instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	(0/2)	(0/2)	(2/2)	(0/2)	True	True
 integron_finder	52965.0	58.0	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.3	integron_finder	2.0.3	(0/1)	(1/1)	(1/1)	(1/1)	True	True
 interproscan	5294.0	554.0	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+iprscan5				Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5				(0/1)	(0/1)	(0/1)	(0/1)	True	True
 iqtree	21598.0	681.0	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	To update	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.1.2	iqtree	2.3.3	(1/1)	(1/1)	(1/1)	(0/1)	True	True
 isescan	57581.0	50.0	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	(0/1)	(1/1)	(1/1)	(1/1)	True	True
-isoformswitchanalyzer	822.0	29.0	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+itsx	868.0	38.0	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 ivar			ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.2	ivar	1.4.2	(5/5)	(5/5)	(5/5)	(5/5)	True	True
 jbrowse	18229.0	2346.0	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	(2/2)	(2/2)	(2/2)	(2/2)	True	True
-jcvi_gff_stats	2469.0	255.0	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)								To update	https://github.com/tanghaibao/jcvi	Sequence Analysis	jcvi_gff_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats	0.8.4	jcvi	1.4.11	(1/1)	(1/1)	(1/1)	(1/1)	True	False
 jellyfish	1138.0	91.0	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	(0/1)	(1/1)	(1/1)	(1/1)	True	True
+kat_filter			kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2	(0/1)	(0/1)	(0/1)	(0/1)	True	True
 kc-align			kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	(1/1)	(0/1)	(1/1)	(0/1)	True	True
 khmer			khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	(8/8)	(8/8)	(8/8)	(0/8)	True	True
 kleborate	319.0	38.0	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	Up-to-date	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	2.3.2	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 kofamscan	594.0	33.0	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	(0/1)	(0/1)	(1/1)	(1/1)	True	True
+kraken	13938.0	404.0	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	(5/5)	(5/5)	(5/5)	(5/5)	True	True
+kraken2	185308.0	2367.0	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.1	kraken2	2.1.3	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+kraken2tax	14683.0	481.0	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk		(1/1)	(1/1)	(1/1)	(0/1)	True	True
 kraken_biom	1444.0	182.0	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0	(0/1)	(1/1)	(1/1)	(1/1)	True	True
 kraken_taxonomy_report	2527.0	354.0	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	(1/1)	(1/1)	(1/1)	(0/1)	True	True
 krakentools			krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	(1/6)	(6/6)	(6/6)	(6/6)	True	True
 krocus			krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-last	227.0	41.0	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	last		LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	https://github.com/galaxyproject/tools-iuc/tree/main/tools/last	1205	last	1542	(0/5)	(0/5)	(5/5)	(5/5)	True	False
+lca_wrapper	137.0	2.0	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 legsta	55.0	7.0	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-length_and_gc_content	4090.0	322.0	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+lighter	152.0	9.0	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 limma_voom	20344.0	1012.0	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 lineagespot	37.0	2.0	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		(0/1)	(0/1)	(1/1)	(0/1)	True	True
-links	405.0	77.0	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	(0/1)	(1/1)	(1/1)	(0/1)	True	False
 lorikeet			lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+lotus2	936.0	114.0	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	Up-to-date	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.32	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 m6anet	3.0		m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 maaslin2	188.0	29.0	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	To update	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	0.99.12	maaslin2	1.16.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-macs2	84202.0	1968.0	macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	macs	macs		MACS	Model-based Analysis of ChIP-seq data.	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	Up-to-date	https://github.com/taoliu/MACS	Sequence Analysis, Statistics	macs2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2	2.2.9.1	macs2	2.2.9.1	(9/9)	(9/9)	(9/9)	(9/9)	True	False
+mafft	143045.0	817.0	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.520	mafft	7.525	(2/2)	(2/2)	(2/2)	(2/2)	True	True
+make_nr			make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.2	biopython	1.70	(0/1)	(0/1)	(0/1)	(0/1)	True	True
 maker	4950.0	419.0	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	(2/2)	(2/2)	(2/2)	(2/2)	True	True
 mapseq	167.0	2.0	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		(0/1)	(0/1)	(1/1)	(0/1)	True	True
 mash	1739.0	12.0	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	(2/2)	(2/2)	(2/2)	(2/2)	True	True
-mashmap			mashmap	Fast local alignment boundaries								Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	Sequence Analysis	mashmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap	3.1.3	mashmap	3.1.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-masigpro	576.0	13.0	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	(1/1)	(0/1)	(1/1)	(0/1)	True	False
 maxbin2	2059.0	118.0	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+maxquant	5804.0	407.0	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	(2/2)	(2/2)	(2/2)	(0/2)	True	True
 mcl	29.0	10.0	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 medaka			medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	1.11.3	(3/4)	(3/4)	(3/4)	(3/4)	True	True
 megahit	9530.0	548.0	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	(1/1)	(1/1)	(1/1)	(1/1)	True	True
@@ -475,45 +149,46 @@ merqury	2483.0	244.0	merqury, merquryplot	Merqury is a tool for evaluating genom
 meryl	6785.0	350.0	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	(0/7)	(0/7)	(0/7)	(0/7)	True	True
 metabat2	4072.0	154.0	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	Up-to-date	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.15	(2/2)	(1/2)	(2/2)	(2/2)	True	True
 metaeuk			metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+metagene_annotator	636.0	115.0	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 metagenomeseq			metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update		Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	(1/1)	(0/1)	(1/1)	(1/1)	True	True
+metanovo	4181.0	15.0	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 metaphlan	10507.0	427.0	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	To update	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.0.6	metaphlan	4.1.0	(1/4)	(2/4)	(4/4)	(4/4)	True	True
+metaquantome			metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	(0/6)	(6/6)	(6/6)	(0/6)	True	True
 metawrapmg			metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	(0/1)	(1/1)	(1/1)	(0/1)	True	True
-migmap	1226.0	7.0	migmap	mapper for full-length T- and B-cell repertoire sequencing	MiGMAP	MiGMAP		MiGMAP	Mapper for full-length T- and B-cell repertoire sequencing.	Sequence analysis, Read mapping	Immunoproteins, genes and antigens, Sequence analysis	Up-to-date	https://github.com/mikessh/migmap	RNA, Sequence Analysis	migmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap	1.0.3	migmap	1.0.3	(1/1)	(0/1)	(1/1)	(0/1)	True	False
 minia	2206.0	109.0	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	(0/1)	(1/1)	(1/1)	(0/1)	True	True
 miniasm	11938.0	178.0	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+minipolish	185.0	21.0	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 miniprot	813.0	15.0	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	(0/2)	(0/2)	(2/2)	(2/2)	True	True
-mirmachine			mirmachine	Tool to detect miRNA in genome sequences								Up-to-date	https://github.com/sinanugur/MirMachine	Sequence Analysis	mirmachine	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine	0.2.13	mirmachine	0.2.13	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-mirnature	10.0	4.0	mirnature	Computational detection of canonical microRNAs								Up-to-date	https://github.com/Bierinformatik/miRNAture	RNA, Sequence Analysis	mirnature	iuc	https://github.com/Bierinformatik/miRNAture	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature	1.1	mirnature	1.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-mitobim	881.0	66.0	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1	(0/1)	(1/1)	(1/1)	(0/1)	True	False
 mitos	32022.0	58.0	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	(1/2)	(1/2)	(2/2)	(0/2)	True	True
 mlst	9304.0	635.0	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	(2/2)	(2/2)	(2/2)	(2/2)	True	True
+mob_suite	89021.0	322.0	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.8	(0/2)	(2/2)	(2/2)	(2/2)	True	True
 mothur			mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	(129/129)	(129/129)	(129/129)	(129/129)	True	True
+mrbayes			mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+msconvert	20406.0	190.0	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			(1/1)	(1/1)	(1/1)	(1/1)	True	True
+msstatstmt	726.0	71.0	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0	(0/1)	(1/1)	(1/1)	(0/1)	True	True
 multigsea	53.0	2.0	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 multiqc	162790.0	8320.0	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.11	multiqc	1.21	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-mummer4			mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mummer4	mummer4						Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1	(6/6)	(6/6)	(6/6)	(6/6)	True	False
 mykrobe			mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-naltorfs			bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)								Up-to-date	https://github.com/BlankenbergLab/nAltORFs	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs	0.1.2	naltorfs	0.1.2	(3/3)	(0/3)	(0/3)	(0/3)	True	False
+mykrobe_parser			mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base		(0/1)	(0/1)	(0/1)	(0/1)	True	True
+mz_to_sqlite	844.0	33.0	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	(1/1)	(1/1)	(1/1)	(0/1)	True	True
 nanocompore			nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	(0/2)	(1/2)	(2/2)	(0/2)	True	True
 nanoplot	63235.0	2195.0	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.42.0	nanoplot	1.42.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 nanopolishcomp			nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	(0/2)	(0/2)	(2/2)	(2/2)	True	True
+ncbi_blast_plus	365597.0	4066.0	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python		(16/18)	(16/18)	(16/18)	(16/18)	True	True
 ncbi_fcs_gx			ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).								Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.0	ncbi-fcs-gx	0.5.0	(1/1)	(0/1)	(1/1)	(0/1)	True	True
-necat	667.0	95.0	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	(0/1)	(0/1)	(1/1)	(0/1)	True	False
 newick_utils	25505.0	448.0	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 nextclade	3527.0	169.0	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	(1/2)	(1/2)	(2/2)	(2/2)	True	True
+nextdenovo	268.0	84.0	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 nonpareil	142.0	5.0	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.4.1	(1/1)	(0/1)	(1/1)	(1/1)	True	True
-novoplasty	6384.0	162.0	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5	(0/1)	(1/1)	(1/1)	(1/1)	True	False
+nucleosome_prediction	861.0	2.0	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 nugen_nudup			nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+obisindicators	45.0	4.0	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base		(1/2)	(0/2)	(2/2)	(1/2)	True	True
 obitools			obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	(0/10)	(10/10)	(10/10)	(10/10)	True	True
-odgi			odgi_build, odgi_viz	Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.								To update	https://github.com/vgteam/odgi	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi	0.3	odgi	0.8.6	(0/2)	(0/2)	(2/2)	(2/2)	True	False
 omark			omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			(0/1)	(0/1)	(1/1)	(1/1)	True	True
-ont_fast5_api			ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3	(0/4)	(0/4)	(4/4)	(0/4)	True	False
-optitype	321.0	24.0	optitype	Precision HLA typing from NGS data								Up-to-date	https://github.com/FRED-2/OptiType	Sequence Analysis	optitype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype	1.3.5	optitype	1.3.5	(0/1)	(0/1)	(1/1)	(0/1)	True	False
 orfipy	774.0	53.0	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	(1/1)	(0/1)	(1/1)	(0/1)	True	True
 orthofinder			orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	Up-to-date	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	2.5.5	(0/1)	(1/1)	(1/1)	(1/1)	True	True
-pairtools			pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats	Flexible tools for Hi-C data processing								Up-to-date	https://pairtools.readthedocs.io	Sequence Analysis	pairtools	iuc	https://github.com/open2c/pairtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools	1.1.0	pairtools	1.1.0	(5/5)	(0/5)	(5/5)	(0/5)	True	False
-pangolin	7276.0	259.0	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	pangolin_cov-lineages	pangolin_cov-lineages		pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages	Tree-based sequence alignment, Variant classification	Virology	Up-to-date	https://github.com/cov-lineages/pangolin	Sequence Analysis	pangolin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin	4.3	pangolin	4.3	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-parse_mito_blast	90.0	31.0	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.								Up-to-date	https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py	Sequence Analysis	parse_mito_blast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast	1.0.2	parse_mito_blast	1.0.2	(1/1)	(1/1)	(1/1)	(0/1)	True	False
-pathview	5260.0	565.0	pathview	Pathview is a tool set for pathway based data integration and visualization.	pathview	pathview		pathview	Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	To update	https://bioconductor.org/packages/release/bioc/html/pathview.html	Statistics, RNA, Micro-array Analysis	pathview	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview	1.34.0	bioconductor-pathview	1.42.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+peptideshaker	17477.0	485.0	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.6	(4/4)	(4/4)	(4/4)	(4/4)	True	True
+pfamscan	165.0	19.0	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 pharokka	2565.0	74.0	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
                 pharokka
             "		(0/1)	(1/1)	(1/1)	(0/1)	True	True
@@ -523,335 +198,166 @@ picrust			picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trai
 picrust2			picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	To update	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.1	picrust2	2.5.2	(0/7)	(7/7)	(7/7)	(0/7)	True	True
 plasflow	22589.0	278.0	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	(1/1)	(1/1)	(1/1)	(0/1)	True	True
 plasmidfinder	22.0	8.0	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	(0/1)	(0/1)	(1/1)	(1/1)	True	True
+plasmidspades			plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	3.15.5	(0/1)	(0/1)	(0/1)	(0/1)	True	True
 polypolish	239.0	24.0	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	(0/1)	(0/1)	(1/1)	(1/1)	True	True
-presto			presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	presto	presto		pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto	0.6.2	presto	0.7.2	(11/11)	(0/11)	(0/11)	(0/11)	True	False
-pretext			pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.								Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext	0.0.6	pretextgraph	0.0.6	(3/3)	(2/3)	(3/3)	(0/3)	True	False
-prinseq	7881.0	70.0	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	(1/1)	(0/1)	(1/1)	(1/1)	True	False
 prodigal			prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	(0/1)	(0/1)	(1/1)	(1/1)	True	True
-progressivemauve	1734.0	286.0	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner								To update		Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve	https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve		progressivemauve	snapshot_2015_02_13	(2/2)	(0/2)	(2/2)	(0/2)	True	False
 prokka	371445.0	3233.0	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-prot-scriber			prot_scriber	Protein annotation of short human readable descriptions								To update	https://github.com/usadellab/prot-scriber	Proteomics	prot_scriber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber	0.1.4	prot-scriber	0.1.5	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+promer			promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python		(0/1)	(0/1)	(0/1)	(0/1)	True	True
 proteinortho	2092.0	125.0	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	Up-to-date	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.1	(0/3)	(0/3)	(3/3)	(0/3)	True	True
-pureclip	1423.0	36.0	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data								To update	https://github.com/skrakau/PureCLIP	Sequence Analysis, RNA, CLIP-seq	pureclip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip	1.0.4	pureclip	1.3.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-purge_dups	16800.0	167.0	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	(1/1)	(1/1)	(1/1)	(0/1)	True	False
 pycoqc	21123.0	350.0	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 pygenometracks	11332.0	377.0	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-pysradb			pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	pysradb	pysradb		pysradb	Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	To update	https://github.com/saketkc/pysradb	Sequence Analysis	pysradb_search	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb	1.4.2	pysradb	2.2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
 qiime_add_on			qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	(0/2)	(0/2)	(2/2)	(2/2)	True	True
 qiime_core			qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis								To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	(0/32)	(0/32)	(32/32)	(32/32)	True	True
-qq_tools			qq_manhattan									To update	https://CRAN.R-project.org/package=qqman	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools	0.1.0	r-qqman	0.1.4	(0/1)	(0/1)	(0/1)	(0/1)	True	False
 qualimap			qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq		qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	To update	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.2.2d	qualimap	2.3	(4/4)	(4/4)	(4/4)	(1/4)	True	True
 quast	51567.0	3567.0	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 quickmerge			quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-ragtag	2833.0	237.0	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	(0/1)	(0/1)	(1/1)	(1/1)	True	False
-rapidnj	176.0	14.0	rapidnj	Galaxy wrapper for the RapidNJ tool	rapidnj	rapidnj		RapidNJ	A tool for fast canonical neighbor-joining tree construction.	Phylogenetic tree generation	Phylogeny	Up-to-date	https://birc.au.dk/software/rapidnj/	Phylogenetics	rapidnj	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj	2.3.2	rapidnj	2.3.2	(1/1)	(0/1)	(1/1)	(1/1)	True	False
+rRNA			meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0		(0/1)	(0/1)	(0/1)	(0/1)	True	True
+racon	21353.0	309.0	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 rasusa			rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	0.8.0	rasusa	2.0.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-raven	6902.0	262.0	raven	Raven is a de novo genome assembler for long uncorrected reads.								To update	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.0	raven-assembler	1.8.3	(0/1)	(1/1)	(1/1)	(1/1)	True	False
 raxml	6808.0	383.0	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 read_it_and_keep	3370.0	71.0	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+reago			reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 recentrifuge	331.0	48.0	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.14.0	recentrifuge	1.14.0	(0/1)	(0/1)	(1/1)	(1/1)	True	True
-red	578.0	88.0	red	Red (REpeat Detector)	red	red		RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	https://github.com/galaxyproject/tools-iuc/tree/main/tools/red	2018.09.10	red	2018.09.10	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-repeatmasker			repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	repeatmasker	repeatmasker		RepeatMasker	A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).	Genome annotation	Sequence analysis, Sequence composition, complexity and repeats	Up-to-date	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker	4.1.5	repeatmasker	4.1.5	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-repeatmodeler	1177.0	217.0	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			(1/1)	(1/1)	(1/1)	(1/1)	True	False
-revoluzer			revoluzer_crex, revoluzer_distmat	revoluzer wrappers	revoluzer	revoluzer		revoluzer	Various tools for genome rearrangement analysis. CREx, TreeREx, etc	Structural variation detection	Molecular evolution, Phylogeny	Up-to-date	https://gitlab.com/Bernt/revoluzer/	Phylogenetics	revoluzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer	0.1.6	revoluzer	0.1.6	(0/2)	(0/2)	(2/2)	(0/2)	True	False
-ribowaltz			ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0	(0/2)	(0/2)	(2/2)	(0/2)	True	False
-rnaquast	1110.0	109.0	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.2.3	rnaquast	2.2.3	(1/1)	(0/1)	(1/1)	(1/1)	True	False
+repeatexplorer2			repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8			(0/1)	(0/1)	(1/1)	(0/1)	True	True
 roary	12225.0	656.0	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 rseqc	135036.0	3269.0	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	(22/22)	(22/22)	(22/22)	(22/22)	True	True
-ruvseq	1236.0	76.0	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	(1/1)	(0/1)	(1/1)	(0/1)	True	False
-salsa2			salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+salmon	55161.0	746.0	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	(2/3)	(1/3)	(3/3)	(1/3)	True	True
 sarscov2formatter	173.0	7.0	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0	(1/1)	(0/1)	(1/1)	(0/1)	True	True
 sarscov2summary	140.0	1.0	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5	(1/1)	(0/1)	(1/1)	(0/1)	True	True
-scanpy			scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.9.6	scanpy	1.7.2	(6/6)	(6/6)	(6/6)	(0/6)	True	False
-scater			scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Transcriptomics, RNA, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	(0/5)	(5/5)	(5/5)	(0/5)	True	False
-schicexplorer			schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7	(0/16)	(0/16)	(16/16)	(0/16)	True	False
-scikit-bio			scikit_bio_diversity_beta_diversity	scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics								Up-to-date	http://scikit-bio.org/	Sequence Analysis	scikit_bio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio	0.4.2	scikit-bio	0.4.2	(1/1)	(0/1)	(0/1)	(0/1)	True	False
 scoary	676.0	61.0	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-scpipe	628.0	11.0	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, RNA, Statistics	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	(1/1)	(0/1)	(1/1)	(0/1)	True	False
 semibin	183.0	10.0	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	(0/6)	(0/6)	(6/6)	(1/6)	True	True
-seq2hla	288.0	16.0	seq2hla	Precision HLA typing and expression from RNAseq data	seq2hla	seq2hla		Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla	2.3	seq2hla	2.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-seqcomplexity	68.0	16.0	seqcomplexity	Sequence complexity for raw reads								Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity	0.1.2	seqcomplexity	0.1.2	(1/1)	(0/1)	(1/1)	(0/1)	True	False
 seqkit			seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	To update	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.3.1	seqkit	2.8.1	(0/5)	(2/5)	(3/5)	(2/5)	True	True
 seqprep			seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	(0/1)	(0/1)	(1/1)	(0/1)	True	True
 seqsero2	12.0		seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-seqtk	59668.0	753.0	seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	seqtk	seqtk		seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk	1.4	seqtk	1.4	(15/15)	(15/15)	(15/15)	(15/15)	True	False
-seqwish	271.0		seqwish	Alignment to variation graph inducer								To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish	0.7.5	seqwish	0.7.10	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-seurat	1543.0	66.0	seurat	A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data								To update	https://github.com/satijalab/seurat	Transcriptomics, RNA, Statistics	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	4.3.0.1	r-seurat	3.0.2	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-shasta	763.0	154.0	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.11.1	(0/1)	(1/1)	(1/1)	(0/1)	True	False
 shorah			shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	(0/1)	(0/1)	(0/1)	(0/1)	True	True
 shovill	41600.0	1008.0	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-sickle	14982.0	269.0	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	(1/1)	(0/1)	(1/1)	(1/1)	True	False
-sina	1128.0	42.0	sina	SINA reference based multiple sequence alignment	sina	sina		SINA	Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	Up-to-date	https://sina.readthedocs.io/en/latest/	Sequence Analysis	sina	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina	1.7.2	sina	1.7.2	(1/1)	(0/1)	(1/1)	(0/1)	True	False
-sinto			sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								To update	https://github.com/timoast/sinto	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.9.0	sinto	0.10.0	(2/2)	(0/2)	(2/2)	(0/2)	True	False
-slamdunk	361.0	2.0	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3	(2/2)	(0/2)	(2/2)	(0/2)	True	False
-sleuth	64.0	8.0	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+sistr_cmd	2489.0	133.0	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2	(0/1)	(1/1)	(1/1)	(0/1)	True	True
 smallgenomeutilities			smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.0	smallgenomeutilities	0.4.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-smudgeplot	203.0	22.0	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	Up-to-date	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.2.5	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+smalt			smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6	(0/1)	(0/1)	(0/1)	(0/1)	True	True
 snap			snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	(1/2)	(1/2)	(1/2)	(0/2)	True	True
-sniffles	919.0	58.0	sniffles	Galaxy wrapper for sniffles	sniffles	sniffles		Sniffles	An algorithm for structural variation detection from third generation sequencing alignment.	Sequence analysis, Structural variation detection	DNA structural variation, Sequencing	To update	https://github.com/fritzsedlazeck/Sniffles	Sequence Analysis	sniffles	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles	1.0.12	sniffles	2.3.3	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-snipit	669.0	22.0	snipit	Summarise snps relative to a reference sequence	snipit	snipit		snipit	Summarise snps relative to a reference sequence	Base position variability plotting	Virology	Up-to-date	https://github.com/aineniamh/snipit	Variant Analysis, Sequence Analysis	snipit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	1.2	snipit	1.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
 snippy	105708.0	1372.0	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	(3/3)	(3/3)	(3/3)	(3/3)	True	True
-socru	621.0	13.0	socru	Order and orientation of complete bacterial genomes								To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru	2.1.7	socru	2.2.4	(1/1)	(0/1)	(1/1)	(0/1)	True	False
 sonneityping	1.0	1.0	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+sortmerna	18504.0	376.0	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	Up-to-date	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.6	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 spades	58834.0	2309.0	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	coronaspades, rnaspades, metaspades, rnaviralspades, plasmidspades, metaviralspades, metaplasmidspades, spades, biosyntheticspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	3.15.5	(9/9)	(9/9)	(9/9)	(9/9)	True	True
-spaln	446.0	34.0	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python		(2/2)	(0/2)	(2/2)	(0/2)	True	False
 spotyping	1278.0	12.0	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+sr_bowtie			bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1	(0/1)	(0/1)	(0/1)	(0/1)	True	True
 srst2	205.0	22.0	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.20	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-stacks			stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq	stacks	stacks		Stacks	Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.	Data handling	Mapping, Population genetics	To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis	stacks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks		stacks	2.65	(0/13)	(13/13)	(13/13)	(12/13)	True	False
-stacks2			stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq								To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2	2.55	stacks	2.65	(0/12)	(12/12)	(12/12)	(12/12)	True	False
-star_fusion	1212.0	35.0	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update		Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+srst2	205.0	22.0	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+staramr	12673.0	889.0	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+stringmlst			stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3	(0/1)	(0/1)	(0/1)	(0/1)	True	True
 structure	2623.0	59.0	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date		Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	(0/1)	(0/1)	(1/1)	(1/1)	True	True
-structureharvester			structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method								Up-to-date		Phylogenetics, Variant Analysis	structureharvester	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester	0.6.94	structureharvester	0.6.94	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-syndiva	30.0	2.0	syndiva	SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.								To update		Proteomics	syndiva	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA	https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva	1.0	clustalo	1.2.4	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-tasmanian_mismatch			tasmanian_mismatch	Analysis of positional mismatches								Up-to-date		Sequence Analysis	tasmanian_mismatch	iuc	https://github.com/nebiolabs/tasmanian-mismatch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch	1.0.7	tasmanian-mismatch	1.0.7	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-taxonomy_filter_refseq			taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-taxonomy_krona_chart	27426.0	1801.0	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-tb-profiler			tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	4.4.1	tb-profiler	6.2.0	(1/1)	(1/1)	(1/1)	(0/1)	True	True
-tbl2gff3	1584.0	229.0	tbl2gff3	Table to GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	Convert Formats, Sequence Analysis	tbl2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3	1.2	bcbiogff	0.6.6	(0/1)	(1/1)	(1/1)	(1/1)	True	False
-te_finder	81.0	7.0	te_finder	Transposable element insertions finder	tefinder	tefinder		TEfinder	A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	To update	https://github.com/VistaSohrab/TEfinder	Sequence Analysis	te_finder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder	1.0.1	samtools	1.20	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-telescope			telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-tetoolkit			tetoolkit_tetranscripts	The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.								Up-to-date	http://hammelllab.labsites.cshl.edu/software/	Sequence Analysis	tetoolkit	iuc	https://github.com/mhammell-laboratory/TEtranscripts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit	2.2.3	tetranscripts	2.2.3	(0/1)	(1/1)	(1/1)	(0/1)	True	False
-tetyper	69.0	8.0	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.								Up-to-date	https://github.com/aesheppard/TETyper	Sequence Analysis	tetyper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper	1.1	tetyper	1.1	(1/1)	(0/1)	(1/1)	(0/1)	True	False
-tn93	113.0	7.0	tn93_readreduce, tn93, tn93_cluster, tn93_filter	Compute distances between sequences								To update	https://github.com/veg/tn93/	Sequence Analysis	tn93	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93	1.0.6	tn93	1.0.14	(4/4)	(0/4)	(4/4)	(0/4)	True	False
-tooldistillator			tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.8.4.1	tooldistillator	0.8.4.1	(0/2)	(0/2)	(2/2)	(2/2)	False	
-transdecoder	5468.0	348.0	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-transit			gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	(5/5)	(5/5)	(5/5)	(0/5)	True	True
-transtermhp	229.0	5.0	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	(1/1)	(0/1)	(1/1)	(0/1)	True	True
-trinity	12733.0	678.0	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	Up-to-date	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.1	(9/13)	(13/13)	(13/13)	(13/13)	True	False
-trinotate	1796.0	151.0	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	(1/1)	(1/1)	(1/1)	(0/1)	True	False
-trycycler			trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5	(0/5)	(5/5)	(5/5)	(5/5)	True	True
-tsebra	5.0		tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.4	tsebra	1.1.2.4	(0/1)	(0/1)	(1/1)	(1/1)	True	False
-ucsc_blat			ucsc_blat	Standalone blat sequence search command line tool	blat	blat		BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	To update	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l		https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat	377	ucsc-blat	445	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-umi_tools			umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	To update	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.2	umi_tools	1.1.5	(5/5)	(5/5)	(5/5)	(5/5)	True	False
-unicycler	65732.0	1558.0	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.0	unicycler	0.5.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
-usher	1060.0	5.0	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	(0/2)	(0/2)	(2/2)	(0/2)	True	True
-valet	637.0	20.0	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	(1/1)	(0/1)	(1/1)	(1/1)	True	True
-vapor	3164.0	94.0	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	(1/1)	(0/1)	(1/1)	(0/1)	True	True
-varvamp			varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology	Up-to-date	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-vegan			vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	(3/3)	(0/3)	(3/3)	(0/3)	True	True
-velvet	12218.0	1280.0	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	(2/2)	(2/2)	(2/2)	(2/2)	True	True
-velvet_optimiser			velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	(1/1)	(1/1)	(1/1)	(0/1)	True	True
-verkko	22.0	9.0	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-vg			vg_convert, vg_deconstruct, vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods								To update	https://github.com/vgteam/vg	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg	1.23.0	vg	1.56.0	(0/3)	(0/3)	(3/3)	(3/3)	True	False
-virAnnot			virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers								To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.0.0+galaxy0	biopython	1.70	(0/3)	(0/3)	(3/3)	(3/3)	True	True
-volcanoplot	30946.0	1749.0	volcanoplot	Tool to create a Volcano Plot								To update		Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.5	r-ggplot2	2.2.1	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-vsearch	8507.0	182.0	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.28.1	(8/8)	(8/8)	(8/8)	(8/8)	True	True
-vsnp			vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics	The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.								To update	https://github.com/USDA-VS/vSNP	Sequence Analysis	vsnp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp	3.0.6	pysam	0.22.1	(0/5)	(0/5)	(0/5)	(0/5)	True	False
-weather_app			simple_weather	provides simple weather in text format								To update	http://wttr.in/	Visualization, Web Services	simpleweather	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app	0.1.2	curl		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-windowmasker	85.0		windowmasker_mkcounts, windowmasker_ustat	Identify repetitive regions using WindowMasker								To update	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/	Sequence Analysis	windowmasker	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker	1.0	blast	2.15.0	(0/2)	(2/2)	(2/2)	(0/2)	True	False
-yahs	344.0	64.0	yahs	Yet Another Hi-C scaffolding tool								Up-to-date	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2a.2	(1/1)	(1/1)	(1/1)	(0/1)	True	False
-bamtools	14039.0	208.0	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	(1/1)	(0/1)	(1/1)	(1/1)	True	True
-bamtools_filter	114845.0	1195.0	bamFilter	Filter BAM datasets on various attributes using bamtools filter	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	2.5.2	bamtools	2.5.2	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-bamtools_split	1434.0	47.0	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag	Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	2.5.2	bamtools	2.5.2	(4/4)	(2/4)	(4/4)	(0/4)	True	False
-biotradis			bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	(3/3)	(0/3)	(0/3)	(0/3)	True	True
-kraken	13938.0	404.0	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	(5/5)	(5/5)	(5/5)	(5/5)	True	True
-kraken2	185308.0	2367.0	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.1	kraken2	2.1.3	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+suite_qiime2__alignment			qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__alignment			qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__alignment			qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
 suite_qiime2__alignment			qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
 suite_qiime2__composition			qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.2.0+q2galaxy.2024.2.1			(4/5)	(4/5)	(4/5)	(2/5)	True	True
+suite_qiime2__composition			qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.2.0+q2galaxy.2024.2.1			(4/5)	(4/5)	(4/5)	(2/5)	True	True
+suite_qiime2__composition			qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.2.0+q2galaxy.2024.2.1			(4/5)	(4/5)	(4/5)	(2/5)	True	True
+suite_qiime2__composition			qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.2.0+q2galaxy.2024.2.1			(4/5)	(4/5)	(4/5)	(2/5)	True	True
+suite_qiime2__cutadapt			qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__cutadapt			qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
 suite_qiime2__cutadapt			qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__cutadapt			qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__dada2			qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__dada2			qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
 suite_qiime2__dada2			qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__dada2			qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__deblur			qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__deblur			qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
 suite_qiime2__deblur			qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__deblur			qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__demux			qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.2.0+q2galaxy.2024.2.1			(6/9)	(6/9)	(6/9)	(6/9)	True	True
+suite_qiime2__demux			qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.2.0+q2galaxy.2024.2.1			(6/9)	(6/9)	(6/9)	(6/9)	True	True
 suite_qiime2__demux			qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.2.0+q2galaxy.2024.2.1			(6/9)	(6/9)	(6/9)	(6/9)	True	True
+suite_qiime2__demux			qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.2.0+q2galaxy.2024.2.1			(6/9)	(6/9)	(6/9)	(6/9)	True	True
+suite_qiime2__diversity			qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.2.0+q2galaxy.2024.2.1			(21/22)	(21/22)	(21/22)	(21/22)	True	True
 suite_qiime2__diversity			qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.2.0+q2galaxy.2024.2.1			(21/22)	(21/22)	(21/22)	(21/22)	True	True
+suite_qiime2__diversity			qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.2.0+q2galaxy.2024.2.1			(21/22)	(21/22)	(21/22)	(21/22)	True	True
+suite_qiime2__diversity			qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.2.0+q2galaxy.2024.2.1			(21/22)	(21/22)	(21/22)	(21/22)	True	True
+suite_qiime2__diversity_lib			qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
+suite_qiime2__diversity_lib			qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
+suite_qiime2__diversity_lib			qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
 suite_qiime2__diversity_lib			qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
 suite_qiime2__emperor			qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__emperor			qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__emperor			qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__emperor			qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__feature_classifier			qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.2.0+q2galaxy.2024.2.1			(10/11)	(10/11)	(10/11)	(10/11)	True	True
+suite_qiime2__feature_classifier			qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.2.0+q2galaxy.2024.2.1			(10/11)	(10/11)	(10/11)	(10/11)	True	True
 suite_qiime2__feature_classifier			qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.2.0+q2galaxy.2024.2.1			(10/11)	(10/11)	(10/11)	(10/11)	True	True
+suite_qiime2__feature_classifier			qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.2.0+q2galaxy.2024.2.1			(10/11)	(10/11)	(10/11)	(10/11)	True	True
+suite_qiime2__feature_table			qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.2.2+q2galaxy.2024.2.1			(17/22)	(17/22)	(17/22)	(17/22)	True	True
+suite_qiime2__feature_table			qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.2.2+q2galaxy.2024.2.1			(17/22)	(17/22)	(17/22)	(17/22)	True	True
 suite_qiime2__feature_table			qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.2.2+q2galaxy.2024.2.1			(17/22)	(17/22)	(17/22)	(17/22)	True	True
+suite_qiime2__feature_table			qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.2.2+q2galaxy.2024.2.1			(17/22)	(17/22)	(17/22)	(17/22)	True	True
+suite_qiime2__fragment_insertion			qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
 suite_qiime2__fragment_insertion			qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__fragment_insertion			qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__fragment_insertion			qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__longitudinal			qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.2.0+q2galaxy.2024.2.1			(11/11)	(11/11)	(11/11)	(11/11)	True	True
+suite_qiime2__longitudinal			qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.2.0+q2galaxy.2024.2.1			(11/11)	(11/11)	(11/11)	(11/11)	True	True
+suite_qiime2__longitudinal			qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.2.0+q2galaxy.2024.2.1			(11/11)	(11/11)	(11/11)	(11/11)	True	True
 suite_qiime2__longitudinal			qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.2.0+q2galaxy.2024.2.1			(11/11)	(11/11)	(11/11)	(11/11)	True	True
 suite_qiime2__metadata			qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.2.0+q2galaxy.2024.2.1			(3/4)	(3/4)	(3/4)	(3/4)	True	True
+suite_qiime2__metadata			qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.2.0+q2galaxy.2024.2.1			(3/4)	(3/4)	(3/4)	(3/4)	True	True
+suite_qiime2__metadata			qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.2.0+q2galaxy.2024.2.1			(3/4)	(3/4)	(3/4)	(3/4)	True	True
+suite_qiime2__metadata			qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.2.0+q2galaxy.2024.2.1			(3/4)	(3/4)	(3/4)	(3/4)	True	True
+suite_qiime2__phylogeny			qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
+suite_qiime2__phylogeny			qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
 suite_qiime2__phylogeny			qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
+suite_qiime2__phylogeny			qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
+suite_qiime2__quality_control			qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.2.0+q2galaxy.2024.2.1			(6/10)	(6/10)	(6/10)	(6/10)	True	True
+suite_qiime2__quality_control			qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.2.0+q2galaxy.2024.2.1			(6/10)	(6/10)	(6/10)	(6/10)	True	True
 suite_qiime2__quality_control			qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.2.0+q2galaxy.2024.2.1			(6/10)	(6/10)	(6/10)	(6/10)	True	True
+suite_qiime2__quality_control			qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.2.0+q2galaxy.2024.2.1			(6/10)	(6/10)	(6/10)	(6/10)	True	True
+suite_qiime2__quality_filter			qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.2.0+q2galaxy.2024.2.1			(1/1)	(1/1)	(1/1)	(1/1)	True	True
 suite_qiime2__quality_filter			qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.2.0+q2galaxy.2024.2.1			(1/1)	(1/1)	(1/1)	(1/1)	True	True
-suite_qiime2__rescript			qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.2.2+q2galaxy.2024.2.1			(0/25)	(0/25)	(0/25)	(0/25)	False	
+suite_qiime2__quality_filter			qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.2.0+q2galaxy.2024.2.1			(1/1)	(1/1)	(1/1)	(1/1)	True	True
+suite_qiime2__quality_filter			qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.2.0+q2galaxy.2024.2.1			(1/1)	(1/1)	(1/1)	(1/1)	True	True
+suite_qiime2__rescript			qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.2.2+q2galaxy.2024.2.1			(0/25)	(0/25)	(0/25)	(0/25)	True	True
+suite_qiime2__rescript			qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.2.2+q2galaxy.2024.2.1			(0/25)	(0/25)	(0/25)	(0/25)	True	True
+suite_qiime2__rescript			qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.2.2+q2galaxy.2024.2.1			(0/25)	(0/25)	(0/25)	(0/25)	True	True
+suite_qiime2__rescript			qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.2.2+q2galaxy.2024.2.1			(0/25)	(0/25)	(0/25)	(0/25)	True	True
+suite_qiime2__sample_classifier			qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.2.0+q2galaxy.2024.2.1			(15/15)	(15/15)	(15/15)	(15/15)	True	True
 suite_qiime2__sample_classifier			qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.2.0+q2galaxy.2024.2.1			(15/15)	(15/15)	(15/15)	(15/15)	True	True
+suite_qiime2__sample_classifier			qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.2.0+q2galaxy.2024.2.1			(15/15)	(15/15)	(15/15)	(15/15)	True	True
+suite_qiime2__sample_classifier			qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.2.0+q2galaxy.2024.2.1			(15/15)	(15/15)	(15/15)	(15/15)	True	True
+suite_qiime2__taxa			qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__taxa			qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__taxa			qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
 suite_qiime2__taxa			qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
 suite_qiime2__vsearch			qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.2.0+q2galaxy.2024.2.1			(8/8)	(8/8)	(8/8)	(7/8)	True	True
-suite_qiime2_core__tools			qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.2.1+dist.he188c3c2			(2/3)	(2/3)	(2/3)	(2/3)	True	True
+suite_qiime2__vsearch			qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.2.0+q2galaxy.2024.2.1			(8/8)	(8/8)	(8/8)	(7/8)	True	True
+suite_qiime2__vsearch			qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.2.0+q2galaxy.2024.2.1			(8/8)	(8/8)	(8/8)	(7/8)	True	True
+suite_qiime2__vsearch			qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.2.0+q2galaxy.2024.2.1			(8/8)	(8/8)	(8/8)	(7/8)	True	True
 suite_qiime2_core												To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core				(0/1)	(0/1)	(0/1)	(0/1)	True	True
-frogs			FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis								Up-to-date	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	4.1.0	(0/28)	(0/28)	(0/28)	(28/28)	True	True
-ThermoRawFileParser			thermo_raw_file_converter	Thermo RAW file converter								To update	https://github.com/compomics/ThermoRawFileParser	Proteomics	thermo_raw_file_converter	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	1.3.4	thermorawfileparser	1.4.4	(0/1)	(1/1)	(1/1)	(0/1)	True	False
-bed_to_protein_map	385.0	49.0	bed_to_protein_map	Converts a BED file to a tabular list of exon locations								To update		Proteomics	bed_to_protein_map	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	0.2.0	python		(1/1)	(1/1)	(1/1)	(0/1)	True	False
-blast_plus_remote_blastp			blast_plus_remote_blastp	NCBI BLAST+ with -remote option								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	blast_plus_remote_blastp	galaxyp	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp	2.6.0	blast	2.15.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-bumbershoot			idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch									To update	http://proteowizard.sourceforge.net/	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot	3.0.21142	bumbershoot	3_0_21142_0e4f4a4	(0/5)	(0/5)	(5/5)	(0/5)	True	False
-calisp			calisp	Calgary approach to isotopes in proteomics								Up-to-date	https://github.com/kinestetika/Calisp/	Proteomics	calisp	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp	3.0.13	calisp	3.0.13	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-cardinal			cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots	Statistical and computational tools for analyzing mass spectrometry imaging datasets								To update	http://cardinalmsi.org	Proteomics, Metabolomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	2.10.0	bioconductor-cardinal	3.4.3	(0/11)	(9/11)	(11/11)	(11/11)	True	False
-dbbuilder	4758.0	161.0	dbbuilder	Protein Database Downloader								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	Proteomics	dbbuilder	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	0.3.4	wget		(0/1)	(1/1)	(1/1)	(1/1)	True	False
-decoyfasta	104.0	15.0		Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.								To update		Proteomics	decoyfasta	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta				(0/1)	(0/1)	(0/1)	(0/1)	True	False
-dia_umpire	33.0	2.0	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics								To update	http://diaumpire.sourceforge.net/	Proteomics	dia_umpire	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire	2.1.3	dia_umpire	2.1.6	(0/1)	(1/1)	(1/1)	(0/1)	True	False
-dialignr	40.0	1.0	dialignr	DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.								To update	https://github.com/shubham1637/DIAlignR	Proteomics	dialignr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	1.2.0	bioconductor-dialignr	2.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-diann	15.0	3.0	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.								To update	https://github.com/vdemichev/DiaNN	Proteomics	diann	galaxyp	https://github.com/vdemichev/DiaNN	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann	1.8.1			(0/1)	(1/1)	(1/1)	(0/1)	True	False
-diapysef	245.0	11.0	diapysef	diapysef is a convenience package for working with DIA-PASEF data								To update	https://pypi.org/project/diapysef/	Proteomics	diapysef	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef	0.3.5.0	diapysef	1.0.10	(0/1)	(1/1)	(1/1)	(0/1)	True	False
-diffacto	7.0	5.0	diffacto	Diffacto comparative protein abundance estimation								To update	https://github.com/statisticalbiotechnology/diffacto	Proteomics	diffacto	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	1.0.6	diffacto	1.0.7	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-data_manager_eggnog_mapper	9.0	2.0		downloads eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper				(0/1)	(0/1)	(0/1)	(0/1)	True	False
-data_manager_eggnog_mapper_abspath	1.0			download eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper_abspath	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath				(0/1)	(0/1)	(0/1)	(0/1)	True	False
-eggnog_mapper	30565.0	510.0	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	(3/3)	(3/3)	(3/3)	(3/3)	True	True
-encyclopedia			encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut	Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis								To update	https://bitbucket.org/searleb/encyclopedia/wiki/Home	Proteomics	encyclopedia	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia	1.12.34	encyclopedia	2.12.30	(2/7)	(4/7)	(7/7)	(0/7)	True	False
-fastg2protlib	28.0	1.0	fastg2protlib-peptides, fastg2protlib-validate	Generate FASTA from FASTG								To update	https://github.com/galaxyproteomics/fastg2protlib.git	Proteomics	fastg2protlib	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	1.0.2			(0/2)	(0/2)	(2/2)	(0/2)	True	False
-feature_alignment	18.0	1.0	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy								Up-to-date		Proteomics	feature_alignment	galaxyp	https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment	0.11.0	msproteomicstools	0.11.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-filter_by_fasta_ids	26274.0	426.0	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python		(1/1)	(1/1)	(1/1)	(1/1)	True	False
-flashlfq	645.0	17.0	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	(0/1)	(1/1)	(1/1)	(0/1)	True	True
-hardklor	111.0	2.0	hardklor, kronik	Hardklör								To update		Proteomics	hardklor	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor	2.30.1+galaxy1	hardklor	2.3.2	(0/2)	(0/2)	(2/2)	(0/2)	True	False
-idconvert	122.0	3.0	idconvert	Convert mass spectrometry identification files on linux or MacOSX								To update		Proteomics	idconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert		proteowizard	3_0_9992	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-lfq_protein_quant	111.0	3.0	lfq_protein_quant	Enable protein summarisation and quantitation								To update	https://github.com/compomics/LFQ_galaxy_p	Proteomics	lfq_protein_quant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	1.0	bioconductor-msnbase	2.28.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-maldiquant			maldi_quant_peak_detection, maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.								To update	http://strimmerlab.org/software/maldiquant/	Proteomics	MALDIquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant	1.22.0	r-base		(0/2)	(2/2)	(2/2)	(2/2)	True	False
-map_peptides_to_bed	41.0	1.0	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser								To update		Proteomics	map_peptides_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	0.2	biopython	1.70	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-maxquant	5804.0	407.0	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	(2/2)	(2/2)	(2/2)	(0/2)	True	True
-meta_proteome_analyzer	123.0	10.0	meta_proteome_analyzer	MetaProteomeAnalyzer								Up-to-date	https://github.com/compomics/meta-proteome-analyzer/	Proteomics	meta_proteome_analyzer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	2.0.0	mpa-portable	2.0.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-metagene_annotator	636.0	115.0	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-metanovo	4181.0	15.0	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-metaquantome			metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	(0/6)	(6/6)	(6/6)	(0/6)	True	True
-moFF			proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.								Up-to-date	https://github.com/compomics/moFF	Proteomics	proteomics_moff	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	2.0.3	moff	2.0.3	(0/1)	(1/1)	(1/1)	(0/1)	True	False
-morpheus	140.0	4.0	morpheus	Morpheus MS Search Application								To update		Proteomics	morpheus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	2.255.0	morpheus	288	(0/1)	(1/1)	(1/1)	(0/1)	True	False
-mqppep			mqppep_anova, mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Proteomics	mqppep	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	0.1.19	bioconductor-preprocesscore	1.64.0	(0/2)	(0/2)	(2/2)	(0/2)	True	False
-msconvert	20406.0	190.0	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			(1/1)	(1/1)	(1/1)	(1/1)	True	True
-msgfplus	507.0	5.0	msgfplus	MSGF+								To update		Proteomics	msgfplus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	0.5	msgf_plus	2024.03.26	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-msms_extractor	110.0	1.0	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.								To update		Proteomics	msms_extractor	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor	1.0.0	proteowizard	3_0_9992	(0/1)	(0/1)	(1/1)	(1/1)	True	False
-msstats	2036.0	144.0	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	msstatstmt	msstatstmt		MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	To update	https://github.com/MeenaChoi/MSstats	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	4.0.0	bioconductor-msstats	4.10.0	(1/1)	(1/1)	(1/1)	(0/1)	True	False
-msstatstmt	726.0	71.0	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0	(0/1)	(1/1)	(1/1)	(0/1)	True	True
-mt2mq	270.0	19.0	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome								To update		Proteomics	mt2mq	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq	1.1.0	r-tidyverse		(0/1)	(0/1)	(1/1)	(0/1)	True	False
-mz_to_sqlite	844.0	33.0	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	(1/1)	(1/1)	(1/1)	(0/1)	True	True
-openms			AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, CruxAdapter, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSSimulator, MSstatsConverter, MaRaClusterAdapter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteAdductDecharger, MetaboliteSpectralMatcher, MultiplexResolver, MyriMatchAdapter, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OMSSAAdapter, OpenMSDatabasesInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PTModel, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, RTEvaluation, RTModel, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TransformationEvaluation, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses								To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	2.8	openms	3.1.0	(8/164)	(35/164)	(160/164)	(0/164)	True	False
-pathwaymatcher			reactome_pathwaymatcher	Reactome Pathway Matcher								To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-pep_pointer	498.0	9.0	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.								To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python		(1/1)	(1/1)	(1/1)	(0/1)	True	False
-pepquery	4862.0	23.0	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.								To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-pepquery2	707.0	10.0	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation								Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2	(0/3)	(0/3)	(3/3)	(0/3)	True	False
-peptide_genomic_coordinate	468.0	9.0	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files								To update		Proteomics	peptide_genomic_coordinate	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate	1.0.0	python		(1/1)	(1/1)	(1/1)	(0/1)	True	False
-peptideshaker	17477.0	485.0	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.6	(4/4)	(4/4)	(4/4)	(4/4)	True	True
-pepxml_to_xls				Convert PepXML to Tabular								To update		Proteomics	pepxml_to_xls	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls				(0/1)	(0/1)	(0/1)	(0/1)	True	False
-percolator	368.0	5.0	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator								To update		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator	3.5	percolator	3.6.5	(0/4)	(4/4)	(4/4)	(0/4)	True	False
-pi_db_tools			calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools								To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools	1.3	python		(0/3)	(0/3)	(0/3)	(0/3)	True	False
-pmd_fdr			pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS								To update	https://github.com/slhubler/PMD-FDR-for-Galaxy-P	Proteomics	pmd_fdr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	1.4.0	r-base		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-custom_pro_db	1652.0	57.0	custom_pro_db	CustomProDB								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db	1.22.0	bioconductor-rgalaxy	1.37.1	(1/1)	(1/1)	(1/1)	(1/1)	True	False
-custom_pro_db_annotation_data_manager				CustomProDB Annotation								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db_annotation_data_manager	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager				(0/1)	(0/1)	(0/1)	(0/1)	True	False
-psm2sam			PSMtoSAM	PSM to SAM								To update	https://bioconductor.org/packages/release/bioc/html/proBAMr.html	Proteomics	psm_to_sam	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam	1.3.2.1	r-base		(0/1)	(0/1)	(0/1)	(1/1)	True	False
-translate_bed	643.0	49.0	translate_bed	Translate BED transcript CDS or cDNA in 3 frames								To update	http://rest.ensembl.org/	Proteomics	translate_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	0.1.0			(1/1)	(1/1)	(1/1)	(0/1)	True	False
-proteomiqon_joinquantpepionswithproteins	366.0	4.0	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.								To update	https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html	Proteomics	proteomiqon_joinquantpepionswithproteins	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	0.0.1	proteomiqon-joinquantpepionswithproteins	0.0.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-proteomiqon_labeledproteinquantification	14.0	5.0	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html	Proteomics	proteomiqon_labeledproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	0.0.1	proteomiqon-labeledproteinquantification	0.0.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-proteomiqon_labelfreeproteinquantification	6.0	3.0	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html	Proteomics	proteomiqon_labelfreeproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	0.0.1	proteomiqon-labelfreeproteinquantification	0.0.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-proteomiqon_mzmltomzlite	721.0	5.0	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html	Proteomics	proteomiqon_mzmltomzlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite	0.0.8	proteomiqon-mzmltomzlite	0.0.8	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-proteomiqon_peptidedb	96.0	6.0	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html	Proteomics	proteomiqon_peptidedb	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	0.0.7	proteomiqon-peptidedb	0.0.7	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-proteomiqon_peptidespectrummatching	686.0	4.0	proteomiqon_peptidespectrummatching	Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html	Proteomics	proteomiqon_peptidespectrummatching	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	0.0.7	proteomiqon-peptidespectrummatching	0.0.7	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-proteomiqon_proteininference	89.0	4.0	proteomiqon_proteininference	MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html	Proteomics	proteomiqon_proteininference	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	0.0.7	proteomiqon-proteininference	0.0.7	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-proteomiqon_psmbasedquantification	604.0	4.0	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.								To update	https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html	Proteomics	proteomiqon_psmbasedquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	0.0.8	proteomiqon-psmbasedquantification	0.0.9	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-proteomiqon_psmstatistics	694.0	4.0	proteomiqon_psmstatistics	The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html	Proteomics	proteomiqon_psmstatistics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	0.0.8	proteomiqon-psmstatistics	0.0.8	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-proteore_venn_diagram	15.0		proteore_venn_diagram	ProteoRE JVenn Diagram								To update		Proteomics	proteore_venn_diagram	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram	2021.06.08	python		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-psm_validation	20.0		psmvalidator	Validate PSM from Ion Fragmentation								To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3			(0/1)	(0/1)	(1/1)	(0/1)	True	False
-pyprophet			pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.								To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5	(0/6)	(4/6)	(6/6)	(0/6)	True	False
-pyteomics			mztab2tsv	Tools using the pyteomics library	pyteomics	pyteomics		Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-quantp	230.0	6.0	quantp	Correlation between protein and transcript abundance								To update		Proteomics	quantp	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp	1.1.2	r-data.table	1.11.6	(0/1)	(0/1)	(1/1)	(1/1)	True	False
-quantwiz_iq	32.0	1.0	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ								Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-rawtools	175.0	14.0	rawtools	Raw Tools								To update	https://github.com/kevinkovalchik/RawTools	Proteomics	rawtools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools		rawtools	2.0.4	(0/1)	(1/1)	(1/1)	(0/1)	True	False
-sixgill	293.0	24.0	sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS								Up-to-date		Proteomics, MetaProteomics	sixgill	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	0.2.4	sixgill	0.2.4	(0/4)	(0/4)	(4/4)	(0/4)	True	False
-spectrast2spectrast_irt			gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2spectrast_irt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	0.1.0	msproteomicstools	0.11.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-spectrast2tsv			gp_spectrast2tsv	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2tsv	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	0.1.0	msproteomicstools	0.11.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-translate_bed_sequences	57.0	6.0	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column								To update		Proteomics	translate_bed_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	0.2.0	biopython	1.70	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+suite_qiime2_core												To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core				(0/1)	(0/1)	(0/1)	(0/1)	True	True
+suite_qiime2_core												To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core				(0/1)	(0/1)	(0/1)	(0/1)	True	True
+suite_qiime2_core												To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core				(0/1)	(0/1)	(0/1)	(0/1)	True	True
+suite_qiime2_core__tools			qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.2.1+dist.he188c3c2			(2/3)	(2/3)	(2/3)	(2/3)	True	True
+suite_qiime2_core__tools			qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.2.1+dist.he188c3c2			(2/3)	(2/3)	(2/3)	(2/3)	True	True
+suite_qiime2_core__tools			qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.2.1+dist.he188c3c2			(2/3)	(2/3)	(2/3)	(2/3)	True	True
+suite_qiime2_core__tools			qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.2.1+dist.he188c3c2			(2/3)	(2/3)	(2/3)	(2/3)	True	True
+t2ps	457.0	31.0	Draw_phylogram	Draw phylogeny								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+t2t_report	947.0	26.0	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+t_coffee	8690.0	70.0	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+taxonomy_krona_chart	27426.0	1801.0	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+tb-profiler			tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	4.4.1	tb-profiler	6.2.0	(1/1)	(1/1)	(1/1)	(0/1)	True	True
+tooldistillator			tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.8.4.1	tooldistillator	0.8.4.1	(0/2)	(0/2)	(2/2)	(2/2)	True	True
+transit			gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	(5/5)	(5/5)	(5/5)	(0/5)	True	True
+transtermhp	229.0	5.0	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+trim_galore	238699.0	2334.0	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+trycycler			trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5	(0/5)	(5/5)	(5/5)	(5/5)	True	True
+unicycler	65732.0	1558.0	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.0	unicycler	0.5.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
 unipept	5005.0	115.0	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		(1/1)	(1/1)	(1/1)	(0/1)	True	True
 uniprotxml_downloader	1360.0	79.0	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests		(0/1)	(1/1)	(1/1)	(0/1)	True	True
-validate_fasta_database	86.0	25.0	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-bamparse			bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-blast_to_scaffold			blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-blastparser_and_hits			BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-blastx_to_scaffold			blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-cap3	7766.0	101.0	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011	(0/1)	(1/1)	(1/1)	(0/1)	True	False
-deseq2_normalization			deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-ez_histograms			ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-fisher_test			fishertest	Fisher's exact test on two-column hit lists.								To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-gsc_high_dimensions_visualisation			high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-guppy			guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	0.2.2			(0/1)	(0/1)	(0/1)	(0/1)	True	False
-high_dim_heatmap			high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps								To update	https://github.com/cran/gplots	Visualization	high_dim_heatmap	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap	https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap	3.1.3+galaxy0	r-gplots	2.17.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-mapping_quality_stats			mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file								To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	0.22.0	r-optparse	1.3.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-mircounts			mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar		(0/1)	(1/1)	(0/1)	(0/1)	True	False
-oases			oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-probecoverage			probecoverage	computes and plots read coverage of genomic regions by sequencing datasets								To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	0.22.0	pysam	0.22.1	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-rsem	2273.0	199.0	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3	(0/4)	(0/4)	(1/4)	(0/4)	True	False
-sashimi_plot			sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-small_rna_clusters			small_rna_clusters	clusters small rna reads in alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_clusters	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters	1.3.0	pysam	0.22.1	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-small_rna_maps			small_rna_maps	Generates small read maps from alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_maps	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps	3.1.1	numpy		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-small_rna_signatures			overlapping_reads, signature	Computes the tendency of small RNAs to overlap with each other.								To update	http://artbio.fr	RNA	small_rna_signatures	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures	3.4.2	pysam	0.22.1	(0/2)	(0/2)	(0/2)	(0/2)	True	False
-sr_bowtie			bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-sr_bowtie_dataset_annotation			sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.								To update	http://artbio.fr	RNA	sr_bowtie_dataset_annotation	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation	2.8	bowtie	1.3.1	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-tarfast5			tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-xpore			xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1	(0/2)	(0/2)	(0/2)	(0/2)	True	False
-yac_clipper			yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-EMLassemblyline			eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.1+galaxy0	r-emlassemblyline		(0/9)	(0/9)	(9/9)	(9/9)	True	False
-Ecoregionalization_workflow			ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base		(0/6)	(0/6)	(6/6)	(5/6)	True	False
-Geom_mean_workflow			Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base		(0/3)	(0/3)	(3/3)	(3/3)	True	False
-PAMPA			pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2			(0/5)	(5/5)	(5/5)	(5/5)	True	True
-champ_blocs			cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base		(0/3)	(0/3)	(3/3)	(3/3)	True	False
-consensus_from_alignments			aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences								To update		Sequence Analysis	consalign	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments	https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments	1.0.0	r-bioseq		(0/1)	(0/1)	(1/1)	(1/1)	True	False
-data_exploration			tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles		(0/6)	(0/6)	(6/6)	(6/6)	True	False
-xarray			timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray		(5/6)	(2/6)	(6/6)	(5/6)	True	False
-gdal			gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0			(0/8)	(0/8)	(8/8)	(8/8)	True	False
-interpolation			interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt		(0/1)	(0/1)	(1/1)	(0/1)	True	False
-medenv			iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas		(0/1)	(0/1)	(1/1)	(0/1)	True	False
-obisindicators	45.0	4.0	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base		(1/2)	(0/2)	(2/2)	(1/2)	True	True
-ocean			argo_getdata	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15			(0/1)	(0/1)	(1/1)	(0/1)	True	False
-ogcProcess_otb_bandmath			otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base		(0/1)	(0/1)	(1/1)	(0/1)	True	False
-ogcProcess_otb_meanShiftSmoothing			otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base		(0/1)	(0/1)	(1/1)	(0/1)	True	False
-regionalgam			regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv		(0/7)	(0/7)	(7/7)	(7/7)	True	False
-sdmpredictors			sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-spocc			spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2			(0/1)	(0/1)	(1/1)	(1/1)	True	False
-srs_tools			srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base		(4/7)	(0/7)	(7/7)	(7/7)	True	False
-stoc			stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2			(0/5)	(0/5)	(5/5)	(5/5)	True	False
-vigiechiro			vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1			(0/4)	(0/4)	(4/4)	(4/4)	True	False
-zoo_project_ogc_api_processes			zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base		(0/1)	(0/1)	(1/1)	(0/1)	False	
-climate-stripes			climate_stripes	Create climate stripes from a tabular input file								To update	https://www.climate-lab-book.ac.uk/2018/warming-stripes/	Climate Analysis, Visualization	climate_stripes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	1.0.2	python		(1/1)	(1/1)	(1/1)	(0/1)	True	False
-mean-per-zone			mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python		(0/1)	(0/1)	(1/1)	(0/1)	True	False
-psy-maps			psy_maps	Visualization of regular geographical data on a map with psyplot								To update	https://github.com/Chilipp/psy-maps	Visualization, Climate Analysis	psy_maps	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	1.2.1	python		(0/1)	(0/1)	(1/1)	(0/1)	True	False
-droplet-barcode-plot			_dropletBarcodePlot	Make a cell barcode plot for droplet single-cell RNA-seq QC								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	droplet_barcode_plot	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-barcode-plot	1.6.1+galaxy2	scxa-plots	0.0.1	(1/1)	(0/1)	(1/1)	(0/1)	True	False
-fastq_provider			fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-gtf-2-gene-list			_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	gtf2gene_list	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list	1.52.0+galaxy0	atlas-gene-annotation-manipulation	1.1.1	(1/1)	(1/1)	(1/1)	(0/1)	True	False
-fastq_utils			fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2	(0/2)	(0/2)	(0/2)	(0/2)	True	False
-salmon-kallisto-mtx-to-10x			_salmon_kallisto_mtx_to_10x	Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	salmon_kallisto_mtx_to_10x	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x	0.0.1+galaxy6	scipy		(1/1)	(1/1)	(1/1)	(0/1)	True	False
-cell-types-analysis			ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11	(0/8)	(0/8)	(6/8)	(0/8)	True	False
-data-hca			hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4	(0/1)	(0/1)	(1/1)	(0/1)	True	False
-data-scxa			retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget		(1/1)	(1/1)	(1/1)	(0/1)	True	False
-dropletutils	3934.0	126.0	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5	(2/2)	(0/2)	(2/2)	(0/2)	True	False
-garnett			garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5	(0/7)	(0/7)	(7/7)	(0/7)	True	False
-monocle3			monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9	(9/9)	(0/9)	(9/9)	(0/9)	True	False
-sc3			sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6	(0/7)	(0/7)	(7/7)	(0/7)	True	False
-scanpy			anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301	(17/27)	(27/27)	(27/27)	(0/27)	True	False
-scater			scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5	(0/6)	(1/6)	(6/6)	(0/6)	True	False
-scmap			scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0	(0/7)	(0/7)	(7/7)	(0/7)	True	False
-scpred			scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0	(0/4)	(0/4)	(4/4)	(0/4)	True	False
-seurat	1543.0	66.0	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								Up-to-date	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.0.0	(0/19)	(0/19)	(14/19)	(0/19)	True	False
-mzml_validator			mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.								To update	https://github.com/RECETOX/galaxytools	Metabolomics, Proteomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	0.1.0+galaxy2	lxml		(0/1)	(0/1)	(0/1)	(0/1)	True	False
-consolidate_vcfs			consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	consolidate_vcfs	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-filter_density			filterdensity	Filter out position based on distance between SNVs								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_density	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-filter_stats			filterstat	SNVPhyl filter_stats								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_stats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-filter_vcf			filtervcf	SNVPhyl filter_vcf								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_vcf	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-find_repeats			findrepeat	Find repetitive regions on a reference genome using MUMMer								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	find_repeats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-snv_matrix			snvmatrix	Generate matrix of SNV distances								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	snv_matrix	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-vcf2snvalignment			vcf2snvalignment	Generates multiple alignment of variant calls								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	vcf2snvalignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-verify_map			verify_map	Checks the mapping quality of all BAM(s)								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	verify_map	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
-suite_snvphyl				SNVPhyl suite defining all dependencies for SNVPhyl								To update		Sequence Analysis	suite_snvphyl_1_2_3	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl				(0/1)	(0/1)	(0/1)	(0/1)	True	False
-blast2go	1232.0	101.0	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe		(0/1)	(0/1)	(0/1)	(0/1)	True	True
-blast_rbh	22499.0	121.0	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70	(0/1)	(0/1)	(1/1)	(0/1)	True	True
-blastxml_to_top_descr	264558.0	159.0	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python		(0/1)	(0/1)	(1/1)	(0/1)	True	True
-make_nr			make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.2	biopython	1.70	(0/1)	(0/1)	(0/1)	(0/1)	True	True
-ncbi_blast_plus	365597.0	4066.0	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python		(16/18)	(16/18)	(16/18)	(16/18)	True	True
-suite_qiime2__alignment			qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
-suite_qiime2__composition			qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.2.0+q2galaxy.2024.2.1			(4/5)	(4/5)	(4/5)	(2/5)	True	True
-suite_qiime2__cutadapt			qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
-suite_qiime2__dada2			qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
-suite_qiime2__deblur			qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
-suite_qiime2__demux			qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.2.0+q2galaxy.2024.2.1			(6/9)	(6/9)	(6/9)	(6/9)	True	True
-suite_qiime2__diversity			qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.2.0+q2galaxy.2024.2.1			(21/22)	(21/22)	(21/22)	(21/22)	True	True
-suite_qiime2__diversity_lib			qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
-suite_qiime2__emperor			qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
-suite_qiime2__feature_classifier			qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global									To update	https://github.com/qiime2/q2-feature-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier	2024.2.0+q2galaxy.2024.2.1			(10/11)	(10/11)	(10/11)	(10/11)	True	True
-suite_qiime2__feature_table			qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.2.2+q2galaxy.2024.2.1			(17/22)	(17/22)	(17/22)	(17/22)	True	True
-suite_qiime2__fragment_insertion			qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
-suite_qiime2__longitudinal			qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.2.0+q2galaxy.2024.2.1			(11/11)	(11/11)	(11/11)	(11/11)	True	True
-suite_qiime2__metadata			qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.2.0+q2galaxy.2024.2.1			(3/4)	(3/4)	(3/4)	(3/4)	True	True
-suite_qiime2__phylogeny			qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
-suite_qiime2__quality_control			qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.2.0+q2galaxy.2024.2.1			(6/10)	(6/10)	(6/10)	(6/10)	True	True
-suite_qiime2__quality_filter			qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.2.0+q2galaxy.2024.2.1			(1/1)	(1/1)	(1/1)	(1/1)	True	True
-suite_qiime2__rescript			qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.2.2+q2galaxy.2024.2.1			(0/25)	(0/25)	(0/25)	(0/25)	False	
-suite_qiime2__sample_classifier			qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.2.0+q2galaxy.2024.2.1			(15/15)	(15/15)	(15/15)	(15/15)	True	True
-suite_qiime2__taxa			qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
-suite_qiime2__vsearch			qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.2.0+q2galaxy.2024.2.1			(8/8)	(8/8)	(8/8)	(7/8)	True	True
-suite_qiime2_core__tools			qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.2.1+dist.he188c3c2			(2/3)	(2/3)	(2/3)	(2/3)	True	True
-suite_qiime2_core												To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core				(0/1)	(0/1)	(0/1)	(0/1)	True	True
-frogs			FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis								Up-to-date	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	4.1.0	(0/28)	(0/28)	(0/28)	(28/28)	True	True
+usher	1060.0	5.0	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	(0/2)	(0/2)	(2/2)	(0/2)	True	True
+valet	637.0	20.0	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	(1/1)	(0/1)	(1/1)	(1/1)	True	True
+vapor	3164.0	94.0	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+varvamp			varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology	Up-to-date	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+vegan			vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	(3/3)	(0/3)	(3/3)	(0/3)	True	True
+velvet	12218.0	1280.0	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	(2/2)	(2/2)	(2/2)	(2/2)	True	True
+velvet_optimiser			velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	(1/1)	(1/1)	(1/1)	(0/1)	True	True
+virAnnot			virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers								To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.0.0+galaxy0	biopython	1.70	(0/3)	(0/3)	(3/3)	(3/3)	True	True
+vsearch	8507.0	182.0	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.28.1	(8/8)	(8/8)	(8/8)	(8/8)	True	True
+wtdbg	1660.0	116.0	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	(0/1)	(0/1)	(1/1)	(1/1)	True	True
diff --git a/results/microgalaxy/tools.yml b/results/microgalaxy/tools.yml
new file mode 100644
index 00000000..4ea5fceb
--- /dev/null
+++ b/results/microgalaxy/tools.yml
@@ -0,0 +1,2233 @@
+install_repository_dependencies: true
+install_resolver_dependencies: true
+install_tool_dependencies: true
+tools:
+- name: treebest_best
+  owner: earlhaminst
+  tool_panel_section_label: ''
+- name: ete_gene_csv_finder
+  owner: earlhaminst
+  tool_panel_section_label: ''
+- name: ete_genetree_splitter
+  owner: earlhaminst
+  tool_panel_section_label: ''
+- name: ete_homology_classifier
+  owner: earlhaminst
+  tool_panel_section_label: ''
+- name: ete_init_taxdb
+  owner: earlhaminst
+  tool_panel_section_label: ''
+- name: ete_lineage_generator
+  owner: earlhaminst
+  tool_panel_section_label: ''
+- name: ete3_mod
+  owner: earlhaminst
+  tool_panel_section_label: ''
+- name: ete_species_tree_generator
+  owner: earlhaminst
+  tool_panel_section_label: ''
+- name: lotus2
+  owner: earlhaminst
+  tool_panel_section_label: Sequence feature detection
+- name: abacas
+  owner: nml
+  tool_panel_section_label: ''
+- name: assemblystats
+  owner: nml
+  tool_panel_section_label: ''
+- name: biohansel
+  owner: nml
+  tool_panel_section_label: ''
+- name: combine_stats
+  owner: nml
+  tool_panel_section_label: ''
+- name: CryptoGenotyper
+  owner: nml
+  tool_panel_section_label: ''
+- name: ectyper
+  owner: nml
+  tool_panel_section_label: ''
+- name: filter_spades_repeat
+  owner: nml
+  tool_panel_section_label: ''
+- name: getmlst
+  owner: nml
+  tool_panel_section_label: ''
+- name: hivtrace
+  owner: nml
+  tool_panel_section_label: ''
+- name: kat_@EXECUTABLE@
+  owner: nml
+  tool_panel_section_label: ''
+- name: mob_recon
+  owner: nml
+  tool_panel_section_label: ''
+- name: mob_typer
+  owner: nml
+  tool_panel_section_label: ''
+- name: mrbayes
+  owner: nml
+  tool_panel_section_label: ''
+- name: mykrobe_parseR
+  owner: nml
+  tool_panel_section_label: ''
+- name: plasmidspades
+  owner: nml
+  tool_panel_section_label: ''
+- name: promer4_substitutions
+  owner: nml
+  tool_panel_section_label: ''
+- name: sistr_cmd
+  owner: nml
+  tool_panel_section_label: ''
+- name: smalt
+  owner: nml
+  tool_panel_section_label: ''
+- name: srst2
+  owner: nml
+  tool_panel_section_label: ''
+- name: staramr_search
+  owner: nml
+  tool_panel_section_label: ''
+- name: stringmlst
+  owner: nml
+  tool_panel_section_label: ''
+- name: cd_hit_dup
+  owner: devteam
+  tool_panel_section_label: ''
+- name: multispecies_orthologous_microsats
+  owner: devteam
+  tool_panel_section_label: ''
+- name: qualityFilter
+  owner: devteam
+  tool_panel_section_label: ''
+- name: Fetch Taxonomic Ranks
+  owner: devteam
+  tool_panel_section_label: ''
+- name: Kraken2Tax
+  owner: devteam
+  tool_panel_section_label: ''
+- name: lca1
+  owner: devteam
+  tool_panel_section_label: ''
+- name: Draw_phylogram
+  owner: devteam
+  tool_panel_section_label: ''
+- name: t2t_report
+  owner: devteam
+  tool_panel_section_label: ''
+- name: antismash
+  owner: bgruening
+  tool_panel_section_label: Sequence clustering, Gene prediction, Differential gene
+    expression analysis
+- name: combine_metaphlan_humann
+  owner: bebatut
+  tool_panel_section_label: Aggregation
+- name: compare_humann2_output
+  owner: bebatut
+  tool_panel_section_label: Comparison
+- name: flye
+  owner: bgruening
+  tool_panel_section_label: ''
+- name: format_metaphlan2_output
+  owner: bebatut
+  tool_panel_section_label: Formatting
+- name: ''
+  owner: bgruening
+  tool_panel_section_label: ''
+- name: graphmap_align
+  owner: bgruening
+  tool_panel_section_label: ''
+- name: graphmap_overlap
+  owner: bgruening
+  tool_panel_section_label: ''
+- name: ''
+  owner: bgruening
+  tool_panel_section_label: ''
+- name: itsx
+  owner: bgruening
+  tool_panel_section_label: Sequence feature detection
+- name: lighter
+  owner: bgruening
+  tool_panel_section_label: ''
+- name: rbc_mafft_add
+  owner: rnateam
+  tool_panel_section_label: Multiple sequence alignment
+- name: rbc_mafft
+  owner: rnateam
+  tool_panel_section_label: Multiple sequence alignment
+- name: mcl_clustering
+  owner: bgruening
+  tool_panel_section_label: ''
+- name: minipolish
+  owner: bgruening
+  tool_panel_section_label: Localised reassembly, Read depth analysis
+- name: nextdenovo
+  owner: bgruening
+  tool_panel_section_label: De-novo assembly, Genome assembly
+- name: Nucleosome
+  owner: bgruening
+  tool_panel_section_label: ''
+- name: pfamscan
+  owner: bgruening
+  tool_panel_section_label: Protein sequence analysis
+- name: racon
+  owner: bgruening
+  tool_panel_section_label: Genome assembly, Mapping assembly, Sequence trimming
+- name: infernal_cmalign
+  owner: bgruening
+  tool_panel_section_label: Nucleic acid feature detection
+- name: infernal_cmbuild
+  owner: bgruening
+  tool_panel_section_label: Nucleic acid feature detection
+- name: infernal_cmpress
+  owner: bgruening
+  tool_panel_section_label: Nucleic acid feature detection
+- name: infernal_cmscan
+  owner: bgruening
+  tool_panel_section_label: Nucleic acid feature detection
+- name: infernal_cmsearch
+  owner: bgruening
+  tool_panel_section_label: Nucleic acid feature detection
+- name: infernal_cmstat
+  owner: bgruening
+  tool_panel_section_label: Nucleic acid feature detection
+- name: meta_rna
+  owner: rnateam
+  tool_panel_section_label: ''
+- name: reago
+  owner: rnateam
+  tool_panel_section_label: ''
+- name: bg_sortmerna
+  owner: rnateam
+  tool_panel_section_label: Sequence similarity search, Sequence comparison, Sequence
+    alignment analysis
+- name: alevin
+  owner: bgruening
+  tool_panel_section_label: ''
+- name: salmon
+  owner: bgruening
+  tool_panel_section_label: ''
+- name: salmonquantmerge
+  owner: bgruening
+  tool_panel_section_label: ''
+- name: trim_galore
+  owner: bgruening
+  tool_panel_section_label: Sequence trimming
+- name: wtdbg
+  owner: bgruening
+  tool_panel_section_label: Genome assembly, De-novo assembly
+- name: clinod
+  owner: peterjc
+  tool_panel_section_label: ''
+- name: effectiveT3
+  owner: peterjc
+  tool_panel_section_label: ''
+- name: abricate
+  owner: iuc
+  tool_panel_section_label: Antimicrobial resistance prediction
+- name: abricate_list
+  owner: iuc
+  tool_panel_section_label: Antimicrobial resistance prediction
+- name: abricate_summary
+  owner: iuc
+  tool_panel_section_label: Antimicrobial resistance prediction
+- name: abritamr
+  owner: iuc
+  tool_panel_section_label: ''
+- name: abyss-pe
+  owner: iuc
+  tool_panel_section_label: Genome assembly, De-novo assembly, Scaffolding
+- name: aldex2
+  owner: iuc
+  tool_panel_section_label: Statistical inference
+- name: amplican
+  owner: iuc
+  tool_panel_section_label: Alignment, Standardisation and normalisation
+- name: amrfinderplus
+  owner: iuc
+  tool_panel_section_label: Antimicrobial resistance prediction
+- name: ancombc
+  owner: iuc
+  tool_panel_section_label: DNA barcoding
+- name: artic_guppyplex
+  owner: iuc
+  tool_panel_section_label: Sequence alignment
+- name: artic_minion
+  owner: iuc
+  tool_panel_section_label: Sequence alignment
+- name: bakta
+  owner: iuc
+  tool_panel_section_label: Genome annotation
+- name: bandage_image
+  owner: iuc
+  tool_panel_section_label: Sequence assembly visualisation
+- name: bandage_info
+  owner: iuc
+  tool_panel_section_label: Sequence assembly visualisation
+- name: BayeScan
+  owner: iuc
+  tool_panel_section_label: Statistical inference
+- name: bin_refiner
+  owner: iuc
+  tool_panel_section_label: Read binning, Sequence clustering
+- name: biom_add_metadata
+  owner: iuc
+  tool_panel_section_label: Formatting
+- name: biom_convert
+  owner: iuc
+  tool_panel_section_label: Formatting
+- name: biom_from_uc
+  owner: iuc
+  tool_panel_section_label: Formatting
+- name: biom_normalize_table
+  owner: iuc
+  tool_panel_section_label: Formatting
+- name: biom_subset_table
+  owner: iuc
+  tool_panel_section_label: Formatting
+- name: biom_summarize_table
+  owner: iuc
+  tool_panel_section_label: Formatting
+- name: est_abundance
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: busco
+  owner: iuc
+  tool_panel_section_label: Sequence assembly validation, Scaffolding, Genome assembly,
+    Transcriptome assembly
+- name: cat_add_names
+  owner: iuc
+  tool_panel_section_label: ''
+- name: cat_bins
+  owner: iuc
+  tool_panel_section_label: ''
+- name: cat_contigs
+  owner: iuc
+  tool_panel_section_label: ''
+- name: cat_prepare
+  owner: iuc
+  tool_panel_section_label: ''
+- name: cat_summarise
+  owner: iuc
+  tool_panel_section_label: ''
+- name: cd_hit
+  owner: iuc
+  tool_panel_section_label: Sequence clustering
+- name: cemitool
+  owner: iuc
+  tool_panel_section_label: Enrichment analysis, Pathway or network analysis
+- name: checkm_analyze
+  owner: iuc
+  tool_panel_section_label: Operation
+- name: checkm_lineage_set
+  owner: iuc
+  tool_panel_section_label: Operation
+- name: checkm_lineage_wf
+  owner: iuc
+  tool_panel_section_label: Operation
+- name: checkm_plot
+  owner: iuc
+  tool_panel_section_label: Operation
+- name: checkm_qa
+  owner: iuc
+  tool_panel_section_label: Operation
+- name: checkm_taxon_set
+  owner: iuc
+  tool_panel_section_label: Operation
+- name: checkm_taxonomy_wf
+  owner: iuc
+  tool_panel_section_label: Operation
+- name: checkm_tetra
+  owner: iuc
+  tool_panel_section_label: Operation
+- name: checkm_tree
+  owner: iuc
+  tool_panel_section_label: Operation
+- name: checkm_tree_qa
+  owner: iuc
+  tool_panel_section_label: Operation
+- name: clustalw
+  owner: devteam
+  tool_panel_section_label: ''
+- name: codeml
+  owner: iuc
+  tool_panel_section_label: Probabilistic sequence generation, Phylogenetic tree generation
+    (maximum likelihood and Bayesian methods), Phylogenetic tree analysis
+- name: cooc_mutbamscan
+  owner: iuc
+  tool_panel_section_label: ''
+- name: cooc_pubmut
+  owner: iuc
+  tool_panel_section_label: ''
+- name: cooc_tabmut
+  owner: iuc
+  tool_panel_section_label: ''
+- name: concoct
+  owner: iuc
+  tool_panel_section_label: Sequence clustering, Read binning
+- name: concoct_coverage_table
+  owner: iuc
+  tool_panel_section_label: Sequence clustering, Read binning
+- name: concoct_cut_up_fasta
+  owner: iuc
+  tool_panel_section_label: Sequence clustering, Read binning
+- name: concoct_extract_fasta_bins
+  owner: iuc
+  tool_panel_section_label: Sequence clustering, Read binning
+- name: concoct_merge_cut_up_clustering
+  owner: iuc
+  tool_panel_section_label: Sequence clustering, Read binning
+- name: coverm_contig
+  owner: iuc
+  tool_panel_section_label: Local alignment
+- name: coverm_genome
+  owner: iuc
+  tool_panel_section_label: Local alignment
+- name: cutadapt
+  owner: lparsons
+  tool_panel_section_label: Sequence trimming
+- name: dada2_assignTaxonomyAddspecies
+  owner: iuc
+  tool_panel_section_label: Variant calling, DNA barcoding
+- name: dada2_dada
+  owner: iuc
+  tool_panel_section_label: Variant calling, DNA barcoding
+- name: dada2_filterAndTrim
+  owner: iuc
+  tool_panel_section_label: Variant calling, DNA barcoding
+- name: dada2_learnErrors
+  owner: iuc
+  tool_panel_section_label: Variant calling, DNA barcoding
+- name: dada2_makeSequenceTable
+  owner: iuc
+  tool_panel_section_label: Variant calling, DNA barcoding
+- name: dada2_mergePairs
+  owner: iuc
+  tool_panel_section_label: Variant calling, DNA barcoding
+- name: dada2_plotComplexity
+  owner: iuc
+  tool_panel_section_label: Variant calling, DNA barcoding
+- name: dada2_plotQualityProfile
+  owner: iuc
+  tool_panel_section_label: Variant calling, DNA barcoding
+- name: dada2_removeBimeraDenovo
+  owner: iuc
+  tool_panel_section_label: Variant calling, DNA barcoding
+- name: dada2_seqCounts
+  owner: iuc
+  tool_panel_section_label: Variant calling, DNA barcoding
+- name: Fasta_to_Contig2Bin
+  owner: iuc
+  tool_panel_section_label: Read binning
+- name: das_tool
+  owner: iuc
+  tool_panel_section_label: Read binning
+- name: bg_diamond
+  owner: bgruening
+  tool_panel_section_label: Sequence alignment analysis
+- name: bg_diamond_makedb
+  owner: bgruening
+  tool_panel_section_label: Sequence alignment analysis
+- name: bg_diamond_view
+  owner: bgruening
+  tool_panel_section_label: Sequence alignment analysis
+- name: disco
+  owner: iuc
+  tool_panel_section_label: Protein sequence analysis
+- name: dram_annotate
+  owner: iuc
+  tool_panel_section_label: Gene functional annotation
+- name: dram_distill
+  owner: iuc
+  tool_panel_section_label: Gene functional annotation
+- name: dram_merge_annotations
+  owner: iuc
+  tool_panel_section_label: Gene functional annotation
+- name: dram_neighborhoods
+  owner: iuc
+  tool_panel_section_label: Gene functional annotation
+- name: dram_strainer
+  owner: iuc
+  tool_panel_section_label: Gene functional annotation
+- name: drep_compare
+  owner: iuc
+  tool_panel_section_label: Genome comparison
+- name: drep_dereplicate
+  owner: iuc
+  tool_panel_section_label: Genome comparison
+- name: export2graphlan
+  owner: iuc
+  tool_panel_section_label: Conversion
+- name: fargene
+  owner: iuc
+  tool_panel_section_label: Antimicrobial resistance prediction
+- name: fastp
+  owner: iuc
+  tool_panel_section_label: ''
+- name: fastqe
+  owner: iuc
+  tool_panel_section_label: Sequencing quality control
+- name: fasttree
+  owner: iuc
+  tool_panel_section_label: Phylogenetic tree generation (from molecular sequences),
+    Phylogenetic tree generation (maximum likelihood and Bayesian methods)
+- name: filtlong
+  owner: iuc
+  tool_panel_section_label: ''
+- name: fraggenescan
+  owner: iuc
+  tool_panel_section_label: Gene prediction
+- name: freyja_aggregate_plot
+  owner: iuc
+  tool_panel_section_label: ''
+- name: freyja_boot
+  owner: iuc
+  tool_panel_section_label: ''
+- name: freyja_demix
+  owner: iuc
+  tool_panel_section_label: ''
+- name: freyja_variants
+  owner: iuc
+  tool_panel_section_label: ''
+- name: funannotate_annotate
+  owner: iuc
+  tool_panel_section_label: ''
+- name: funannotate_clean
+  owner: iuc
+  tool_panel_section_label: ''
+- name: funannotate_compare
+  owner: iuc
+  tool_panel_section_label: ''
+- name: funannotate_predict
+  owner: iuc
+  tool_panel_section_label: ''
+- name: funannotate_sort
+  owner: iuc
+  tool_panel_section_label: ''
+- name: glimmer_acgt_content
+  owner: bgruening
+  tool_panel_section_label: Sequence analysis, Genetic variation analysis
+- name: glimmer_build_icm
+  owner: bgruening
+  tool_panel_section_label: Sequence analysis, Genetic variation analysis
+- name: glimmer_extract
+  owner: bgruening
+  tool_panel_section_label: Sequence analysis, Genetic variation analysis
+- name: glimmer_gbk_to_orf
+  owner: bgruening
+  tool_panel_section_label: Sequence analysis, Genetic variation analysis
+- name: glimmer_glimmer_to_gff
+  owner: bgruening
+  tool_panel_section_label: Sequence analysis, Genetic variation analysis
+- name: glimmer_long_orfs
+  owner: bgruening
+  tool_panel_section_label: Sequence analysis, Genetic variation analysis
+- name: glimmer_knowledge_based
+  owner: bgruening
+  tool_panel_section_label: Sequence analysis, Genetic variation analysis
+- name: glimmer_not_knowledge_based
+  owner: bgruening
+  tool_panel_section_label: Sequence analysis, Genetic variation analysis
+- name: goenrichment
+  owner: iuc
+  tool_panel_section_label: Gene-set enrichment analysis
+- name: goslimmer
+  owner: iuc
+  tool_panel_section_label: Gene-set enrichment analysis
+- name: goseq
+  owner: iuc
+  tool_panel_section_label: Gene functional annotation
+- name: graphlan
+  owner: iuc
+  tool_panel_section_label: Phylogenetic inference, Phylogenetic tree visualisation,
+    Phylogenetic tree editing, Taxonomic classification
+- name: graphlan_annotate
+  owner: iuc
+  tool_panel_section_label: Phylogenetic inference, Phylogenetic tree visualisation,
+    Phylogenetic tree editing, Taxonomic classification
+- name: gtdbtk_classify_wf
+  owner: iuc
+  tool_panel_section_label: Genome alignment, Taxonomic classification, Sequence assembly,
+    Query and retrieval
+- name: gubbins
+  owner: iuc
+  tool_panel_section_label: Genotyping, Phylogenetic inference, Ancestral reconstruction
+- name: hamronize_summarize
+  owner: iuc
+  tool_panel_section_label: Data handling, Antimicrobial resistance prediction, Parsing
+- name: hamronize_tool
+  owner: iuc
+  tool_panel_section_label: Data handling, Antimicrobial resistance prediction, Parsing
+- name: bio_hansel
+  owner: iuc
+  tool_panel_section_label: Genotyping, SNP detection, Genome assembly
+- name: hifiasm_meta
+  owner: galaxy-australia
+  tool_panel_section_label: Sequence assembly
+- name: hmmer_alimask
+  owner: iuc
+  tool_panel_section_label: Formatting, Multiple sequence alignment, Sequence profile
+    generation, Format validation, Conversion, Sequence generation, Data retrieval,
+    Statistical calculation, Database search, Formatting, Database search, Database
+    search, Probabilistic sequence generation, Statistical calculation, Statistical
+    calculation, Sequence database search, Formatting, Sequence database search, Database
+    search, Sequence database search
+- name: hmmer_hmmalign
+  owner: iuc
+  tool_panel_section_label: Formatting, Multiple sequence alignment, Sequence profile
+    generation, Format validation, Conversion, Sequence generation, Data retrieval,
+    Statistical calculation, Database search, Formatting, Database search, Database
+    search, Probabilistic sequence generation, Statistical calculation, Statistical
+    calculation, Sequence database search, Formatting, Sequence database search, Database
+    search, Sequence database search
+- name: hmmer_hmmbuild
+  owner: iuc
+  tool_panel_section_label: Formatting, Multiple sequence alignment, Sequence profile
+    generation, Format validation, Conversion, Sequence generation, Data retrieval,
+    Statistical calculation, Database search, Formatting, Database search, Database
+    search, Probabilistic sequence generation, Statistical calculation, Statistical
+    calculation, Sequence database search, Formatting, Sequence database search, Database
+    search, Sequence database search
+- name: hmmer_hmmconvert
+  owner: iuc
+  tool_panel_section_label: Formatting, Multiple sequence alignment, Sequence profile
+    generation, Format validation, Conversion, Sequence generation, Data retrieval,
+    Statistical calculation, Database search, Formatting, Database search, Database
+    search, Probabilistic sequence generation, Statistical calculation, Statistical
+    calculation, Sequence database search, Formatting, Sequence database search, Database
+    search, Sequence database search
+- name: hmmer_hmmemit
+  owner: iuc
+  tool_panel_section_label: Formatting, Multiple sequence alignment, Sequence profile
+    generation, Format validation, Conversion, Sequence generation, Data retrieval,
+    Statistical calculation, Database search, Formatting, Database search, Database
+    search, Probabilistic sequence generation, Statistical calculation, Statistical
+    calculation, Sequence database search, Formatting, Sequence database search, Database
+    search, Sequence database search
+- name: hmmer_hmmfetch
+  owner: iuc
+  tool_panel_section_label: Formatting, Multiple sequence alignment, Sequence profile
+    generation, Format validation, Conversion, Sequence generation, Data retrieval,
+    Statistical calculation, Database search, Formatting, Database search, Database
+    search, Probabilistic sequence generation, Statistical calculation, Statistical
+    calculation, Sequence database search, Formatting, Sequence database search, Database
+    search, Sequence database search
+- name: hmmer_hmmscan
+  owner: iuc
+  tool_panel_section_label: Formatting, Multiple sequence alignment, Sequence profile
+    generation, Format validation, Conversion, Sequence generation, Data retrieval,
+    Statistical calculation, Database search, Formatting, Database search, Database
+    search, Probabilistic sequence generation, Statistical calculation, Statistical
+    calculation, Sequence database search, Formatting, Sequence database search, Database
+    search, Sequence database search
+- name: hmmer_hmmsearch
+  owner: iuc
+  tool_panel_section_label: Formatting, Multiple sequence alignment, Sequence profile
+    generation, Format validation, Conversion, Sequence generation, Data retrieval,
+    Statistical calculation, Database search, Formatting, Database search, Database
+    search, Probabilistic sequence generation, Statistical calculation, Statistical
+    calculation, Sequence database search, Formatting, Sequence database search, Database
+    search, Sequence database search
+- name: hmmer_jackhmmer
+  owner: iuc
+  tool_panel_section_label: Formatting, Multiple sequence alignment, Sequence profile
+    generation, Format validation, Conversion, Sequence generation, Data retrieval,
+    Statistical calculation, Database search, Formatting, Database search, Database
+    search, Probabilistic sequence generation, Statistical calculation, Statistical
+    calculation, Sequence database search, Formatting, Sequence database search, Database
+    search, Sequence database search
+- name: hmmer_nhmmer
+  owner: iuc
+  tool_panel_section_label: Formatting, Multiple sequence alignment, Sequence profile
+    generation, Format validation, Conversion, Sequence generation, Data retrieval,
+    Statistical calculation, Database search, Formatting, Database search, Database
+    search, Probabilistic sequence generation, Statistical calculation, Statistical
+    calculation, Sequence database search, Formatting, Sequence database search, Database
+    search, Sequence database search
+- name: hmmer_nhmmscan
+  owner: iuc
+  tool_panel_section_label: Formatting, Multiple sequence alignment, Sequence profile
+    generation, Format validation, Conversion, Sequence generation, Data retrieval,
+    Statistical calculation, Database search, Formatting, Database search, Database
+    search, Probabilistic sequence generation, Statistical calculation, Statistical
+    calculation, Sequence database search, Formatting, Sequence database search, Database
+    search, Sequence database search
+- name: hmmer_phmmer
+  owner: iuc
+  tool_panel_section_label: Formatting, Multiple sequence alignment, Sequence profile
+    generation, Format validation, Conversion, Sequence generation, Data retrieval,
+    Statistical calculation, Database search, Formatting, Database search, Database
+    search, Probabilistic sequence generation, Statistical calculation, Statistical
+    calculation, Sequence database search, Formatting, Sequence database search, Database
+    search, Sequence database search
+- name: humann
+  owner: iuc
+  tool_panel_section_label: Species frequency estimation, Taxonomic classification,
+    Phylogenetic analysis
+- name: humann_associate
+  owner: iuc
+  tool_panel_section_label: Species frequency estimation, Taxonomic classification,
+    Phylogenetic analysis
+- name: humann_barplot
+  owner: iuc
+  tool_panel_section_label: Species frequency estimation, Taxonomic classification,
+    Phylogenetic analysis
+- name: humann_join_tables
+  owner: iuc
+  tool_panel_section_label: Species frequency estimation, Taxonomic classification,
+    Phylogenetic analysis
+- name: humann_reduce_table
+  owner: iuc
+  tool_panel_section_label: Species frequency estimation, Taxonomic classification,
+    Phylogenetic analysis
+- name: humann_regroup_table
+  owner: iuc
+  tool_panel_section_label: Species frequency estimation, Taxonomic classification,
+    Phylogenetic analysis
+- name: humann_rename_table
+  owner: iuc
+  tool_panel_section_label: Species frequency estimation, Taxonomic classification,
+    Phylogenetic analysis
+- name: humann_renorm_table
+  owner: iuc
+  tool_panel_section_label: Species frequency estimation, Taxonomic classification,
+    Phylogenetic analysis
+- name: humann_rna_dna_norm
+  owner: iuc
+  tool_panel_section_label: Species frequency estimation, Taxonomic classification,
+    Phylogenetic analysis
+- name: humann_split_stratified_table
+  owner: iuc
+  tool_panel_section_label: Species frequency estimation, Taxonomic classification,
+    Phylogenetic analysis
+- name: humann_split_table
+  owner: iuc
+  tool_panel_section_label: Species frequency estimation, Taxonomic classification,
+    Phylogenetic analysis
+- name: humann_strain_profiler
+  owner: iuc
+  tool_panel_section_label: Species frequency estimation, Taxonomic classification,
+    Phylogenetic analysis
+- name: humann_unpack_pathways
+  owner: iuc
+  tool_panel_section_label: Species frequency estimation, Taxonomic classification,
+    Phylogenetic analysis
+- name: hyphy_absrel
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_annotate
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_bgm
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_busted
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_cfel
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_conv
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_fade
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_fel
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_fubar
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_gard
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_meme
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_prime
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_relax
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_slac
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_sm19
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_strike_ambigs
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hyphy_summary
+  owner: iuc
+  tool_panel_section_label: Statistical calculation
+- name: hypo
+  owner: iuc
+  tool_panel_section_label: Optimisation and refinement, Genome assembly
+- name: icescreen
+  owner: iuc
+  tool_panel_section_label: Database search, Protein feature detection
+- name: idba_hybrid
+  owner: iuc
+  tool_panel_section_label: Sequence assembly
+- name: idba_tran
+  owner: iuc
+  tool_panel_section_label: Sequence assembly
+- name: idba_ud
+  owner: iuc
+  tool_panel_section_label: Sequence assembly
+- name: instrain_compare
+  owner: iuc
+  tool_panel_section_label: SNP detection, Genome comparison
+- name: instrain_profile
+  owner: iuc
+  tool_panel_section_label: SNP detection, Genome comparison
+- name: interproscan
+  owner: bgruening
+  tool_panel_section_label: Sequence motif recognition, Protein feature detection
+- name: iqtree
+  owner: iuc
+  tool_panel_section_label: ''
+- name: ivar_consensus
+  owner: iuc
+  tool_panel_section_label: ''
+- name: ivar_filtervariants
+  owner: iuc
+  tool_panel_section_label: ''
+- name: ivar_removereads
+  owner: iuc
+  tool_panel_section_label: ''
+- name: ivar_trim
+  owner: iuc
+  tool_panel_section_label: ''
+- name: ivar_variants
+  owner: iuc
+  tool_panel_section_label: ''
+- name: jbrowse_to_standalone
+  owner: iuc
+  tool_panel_section_label: Genome visualisation
+- name: jbrowse
+  owner: iuc
+  tool_panel_section_label: Genome visualisation
+- name: jellyfish
+  owner: iuc
+  tool_panel_section_label: k-mer counting
+- name: kc-align
+  owner: iuc
+  tool_panel_section_label: Multiple sequence alignment
+- name: khmer_abundance_distribution_single
+  owner: iuc
+  tool_panel_section_label: Standardisation and normalisation, De-novo assembly
+- name: khmer_abundance_distribution
+  owner: iuc
+  tool_panel_section_label: Standardisation and normalisation, De-novo assembly
+- name: khmer_count_median
+  owner: iuc
+  tool_panel_section_label: Standardisation and normalisation, De-novo assembly
+- name: khmer_partition
+  owner: iuc
+  tool_panel_section_label: Standardisation and normalisation, De-novo assembly
+- name: khmer_extract_partitions
+  owner: iuc
+  tool_panel_section_label: Standardisation and normalisation, De-novo assembly
+- name: khmer_filter_abundance
+  owner: iuc
+  tool_panel_section_label: Standardisation and normalisation, De-novo assembly
+- name: khmer_filter_below_abundance_cutoff
+  owner: iuc
+  tool_panel_section_label: Standardisation and normalisation, De-novo assembly
+- name: khmer_normalize_by_median
+  owner: iuc
+  tool_panel_section_label: Standardisation and normalisation, De-novo assembly
+- name: kleborate
+  owner: iuc
+  tool_panel_section_label: Multilocus sequence typing, Genome assembly, Virulence
+    prediction
+- name: kofamscan
+  owner: iuc
+  tool_panel_section_label: ''
+- name: kraken_biom
+  owner: iuc
+  tool_panel_section_label: ''
+- name: kraken_taxonomy_report
+  owner: iuc
+  tool_panel_section_label: ''
+- name: krakentools_alpha_diversity
+  owner: iuc
+  tool_panel_section_label: Visualisation, Aggregation
+- name: krakentools_beta_diversity
+  owner: iuc
+  tool_panel_section_label: Visualisation, Aggregation
+- name: krakentools_combine_kreports
+  owner: iuc
+  tool_panel_section_label: Visualisation, Aggregation
+- name: krakentools_extract_kraken_reads
+  owner: iuc
+  tool_panel_section_label: Visualisation, Aggregation
+- name: krakentools_kreport2krona
+  owner: iuc
+  tool_panel_section_label: Visualisation, Aggregation
+- name: krakentools_kreport2mpa
+  owner: iuc
+  tool_panel_section_label: Visualisation, Aggregation
+- name: krocus
+  owner: iuc
+  tool_panel_section_label: ''
+- name: legsta
+  owner: iuc
+  tool_panel_section_label: ''
+- name: lineagespot
+  owner: iuc
+  tool_panel_section_label: Variant calling
+- name: lorikeet_spoligotype
+  owner: iuc
+  tool_panel_section_label: ''
+- name: m6anet
+  owner: iuc
+  tool_panel_section_label: Quantification, Imputation, Gene expression profiling
+- name: maaslin2
+  owner: iuc
+  tool_panel_section_label: ''
+- name: maker
+  owner: iuc
+  tool_panel_section_label: Genome annotation
+- name: maker_map_ids
+  owner: iuc
+  tool_panel_section_label: Genome annotation
+- name: mapseq
+  owner: iuc
+  tool_panel_section_label: ''
+- name: mash_screen
+  owner: iuc
+  tool_panel_section_label: Sequence distance matrix generation
+- name: mash_sketch
+  owner: iuc
+  tool_panel_section_label: Sequence distance matrix generation
+- name: maxbin2
+  owner: mbernt
+  tool_panel_section_label: Sequence assembly
+- name: mcl
+  owner: iuc
+  tool_panel_section_label: Clustering, Network analysis, Gene regulatory network
+    analysis
+- name: medaka_consensus
+  owner: iuc
+  tool_panel_section_label: Base-calling, Variant calling, Sequence assembly
+- name: medaka_consensus_pipeline
+  owner: iuc
+  tool_panel_section_label: Base-calling, Variant calling, Sequence assembly
+- name: medaka_snp
+  owner: iuc
+  tool_panel_section_label: Base-calling, Variant calling, Sequence assembly
+- name: medaka_variant
+  owner: iuc
+  tool_panel_section_label: Base-calling, Variant calling, Sequence assembly
+- name: megahit
+  owner: iuc
+  tool_panel_section_label: Genome assembly
+- name: megahit_contig2fastg
+  owner: iuc
+  tool_panel_section_label: Genome assembly
+- name: megan_blast2lca
+  owner: iuc
+  tool_panel_section_label: Sequence analysis, Taxonomic classification
+- name: megan_blast2rma
+  owner: iuc
+  tool_panel_section_label: Sequence analysis, Taxonomic classification
+- name: megan_daa2info
+  owner: iuc
+  tool_panel_section_label: Sequence analysis, Taxonomic classification
+- name: megan_daa2rma
+  owner: iuc
+  tool_panel_section_label: Sequence analysis, Taxonomic classification
+- name: megan_daa_meganizer
+  owner: iuc
+  tool_panel_section_label: Sequence analysis, Taxonomic classification
+- name: megan_read_extractor
+  owner: iuc
+  tool_panel_section_label: Sequence analysis, Taxonomic classification
+- name: megan_sam2rma
+  owner: iuc
+  tool_panel_section_label: Sequence analysis, Taxonomic classification
+- name: meningotype
+  owner: iuc
+  tool_panel_section_label: ''
+- name: merqury
+  owner: iuc
+  tool_panel_section_label: Genome assembly, k-mer counting, Scaffolding, Phasing,
+    De-novo assembly
+- name: meryl
+  owner: iuc
+  tool_panel_section_label: k-mer counting
+- name: metabat2_jgi_summarize_bam_contig_depths
+  owner: iuc
+  tool_panel_section_label: Read binning, Sequence assembly, Genome annotation
+- name: metabat2
+  owner: iuc
+  tool_panel_section_label: Read binning, Sequence assembly, Genome annotation
+- name: metaeuk_easy_predict
+  owner: iuc
+  tool_panel_section_label: Homology-based gene prediction
+- name: metagenomeseq_normalizaton
+  owner: iuc
+  tool_panel_section_label: Sequence visualisation, Statistical calculation
+- name: customize_metaphlan_database
+  owner: iuc
+  tool_panel_section_label: Nucleic acid sequence analysis, Phylogenetic tree analysis
+- name: extract_metaphlan_database
+  owner: iuc
+  tool_panel_section_label: Nucleic acid sequence analysis, Phylogenetic tree analysis
+- name: merge_metaphlan_tables
+  owner: iuc
+  tool_panel_section_label: Nucleic acid sequence analysis, Phylogenetic tree analysis
+- name: metaphlan
+  owner: iuc
+  tool_panel_section_label: Nucleic acid sequence analysis, Phylogenetic tree analysis
+- name: minia
+  owner: iuc
+  tool_panel_section_label: Genome assembly
+- name: miniasm
+  owner: iuc
+  tool_panel_section_label: ''
+- name: miniprot
+  owner: iuc
+  tool_panel_section_label: ''
+- name: miniprot_index
+  owner: iuc
+  tool_panel_section_label: ''
+- name: mitos
+  owner: iuc
+  tool_panel_section_label: Genome annotation
+- name: mitos2
+  owner: iuc
+  tool_panel_section_label: Genome annotation
+- name: mlst
+  owner: iuc
+  tool_panel_section_label: Taxonomic classification
+- name: mlst_list
+  owner: iuc
+  tool_panel_section_label: Taxonomic classification
+- name: mothur_align_check
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_align_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_amova
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_anosim
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_bin_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_biom_info
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_chimera_bellerophon
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_chimera_ccode
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_chimera_check
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_chimera_perseus
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_chimera_pintail
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_chimera_slayer
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_chimera_uchime
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_chimera_vsearch
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_chop_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_classify_otu
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_classify_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_classify_tree
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_clearcut
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_cluster_classic
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_cluster_fragments
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_cluster_split
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_cluster
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_collect_shared
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_collect_single
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_consensus_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_cooccurrence
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_corr_axes
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_count_groups
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_count_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_create_database
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_degap_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_deunique_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_deunique_tree
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_dist_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_dist_shared
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_fastq_info
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_filter_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_filter_shared
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_communitytype
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_coremicrobiome
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_dists
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_group
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_groups
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_label
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_lineage
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_mimarkspackage
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_otulabels
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_otulist
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_oturep
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_otus
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_rabund
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_relabund
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_sabund
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_get_sharedseqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_heatmap_bin
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_heatmap_sim
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_homova
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_indicator
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_lefse
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_libshuff
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_list_otulabels
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_list_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_make_biom
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_make_contigs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_make_design
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_make_fastq
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_make_group
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_make_lefse
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_make_lookup
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_make_shared
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_make_sra
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_mantel
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_merge_count
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_merge_files
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_merge_groups
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_merge_sfffiles
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_merge_taxsummary
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_metastats
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_mimarks_attributes
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_nmds
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_normalize_shared
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_otu_association
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_otu_hierarchy
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_pairwise_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_parse_list
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_parsimony
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_pca
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_pcoa
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_pcr_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_phylo_diversity
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_phylotype
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_pre_cluster
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_primer_design
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_rarefaction_shared
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_rarefaction_single
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_remove_dists
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_remove_groups
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_remove_lineage
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_remove_otulabels
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_remove_otus
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_remove_rare
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_remove_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_rename_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_reverse_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_screen_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_sens_spec
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_seq_error
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_sffinfo
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_shhh_flows
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_shhh_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_sort_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_split_abund
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_split_groups
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_sub_sample
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_summary_qual
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_summary_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_summary_shared
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_summary_single
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_summary_tax
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_taxonomy_to_krona
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_tree_shared
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_trim_flows
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_trim_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_unifrac_unweighted
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_unifrac_weighted
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_unique_seqs
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: mothur_venn
+  owner: iuc
+  tool_panel_section_label: DNA barcoding, Sequencing quality control, Sequence clustering,
+    Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic
+    analysis
+- name: multigsea
+  owner: iuc
+  tool_panel_section_label: Gene-set enrichment analysis, Aggregation, Pathway analysis
+- name: multiqc
+  owner: iuc
+  tool_panel_section_label: Validation
+- name: mykrobe_predict
+  owner: iuc
+  tool_panel_section_label: Antimicrobial resistance prediction, Variant calling,
+    Genotyping, Sequence trimming
+- name: nanocompore_db
+  owner: iuc
+  tool_panel_section_label: Post-translation modification site prediction, PolyA signal
+    detection, Genotyping, k-mer counting
+- name: nanocompore_sampcomp
+  owner: iuc
+  tool_panel_section_label: Post-translation modification site prediction, PolyA signal
+    detection, Genotyping, k-mer counting
+- name: nanoplot
+  owner: iuc
+  tool_panel_section_label: ''
+- name: nanopolishcomp_eventaligncollapse
+  owner: iuc
+  tool_panel_section_label: ''
+- name: nanopolishcomp_freqmethcalculate
+  owner: iuc
+  tool_panel_section_label: ''
+- name: newick_display
+  owner: iuc
+  tool_panel_section_label: Phylogenetic tree generation, Phylogenetic tree analysis,
+    Phylogenetic tree reconstruction
+- name: nextalign
+  owner: iuc
+  tool_panel_section_label: ''
+- name: nextclade
+  owner: iuc
+  tool_panel_section_label: ''
+- name: nonpareil
+  owner: iuc
+  tool_panel_section_label: ''
+- name: nugen_nudup
+  owner: iuc
+  tool_panel_section_label: ''
+- name: orfipy
+  owner: iuc
+  tool_panel_section_label: Coding region prediction, Database search, Transcriptome
+    assembly, De-novo assembly
+- name: orthofinder_onlygroups
+  owner: iuc
+  tool_panel_section_label: Genome comparison, Phylogenetic tree generation (from
+    molecular sequences), Phylogenetic tree analysis, Genome alignment
+- name: pharokka
+  owner: iuc
+  tool_panel_section_label: ''
+- name: phyloseq_from_dada2
+  owner: iuc
+  tool_panel_section_label: Deposition, Analysis, Visualisation
+- name: phyloseq_plot_ordination
+  owner: iuc
+  tool_panel_section_label: Deposition, Analysis, Visualisation
+- name: phyloseq_plot_richness
+  owner: iuc
+  tool_panel_section_label: Deposition, Analysis, Visualisation
+- name: phyml
+  owner: iuc
+  tool_panel_section_label: Phylogenetic tree generation (maximum likelihood and Bayesian
+    methods)
+- name: picrust_categorize
+  owner: iuc
+  tool_panel_section_label: Phylogenetic reconstruction, Expression analysis, Genome
+    annotation, DNA barcoding
+- name: picrust_compare_biom
+  owner: iuc
+  tool_panel_section_label: Phylogenetic reconstruction, Expression analysis, Genome
+    annotation, DNA barcoding
+- name: picrust_format_tree_and_trait_table
+  owner: iuc
+  tool_panel_section_label: Phylogenetic reconstruction, Expression analysis, Genome
+    annotation, DNA barcoding
+- name: picrust_metagenome_contributions
+  owner: iuc
+  tool_panel_section_label: Phylogenetic reconstruction, Expression analysis, Genome
+    annotation, DNA barcoding
+- name: picrust_normalize_by_copy_number
+  owner: iuc
+  tool_panel_section_label: Phylogenetic reconstruction, Expression analysis, Genome
+    annotation, DNA barcoding
+- name: picrust_predict_metagenomes
+  owner: iuc
+  tool_panel_section_label: Phylogenetic reconstruction, Expression analysis, Genome
+    annotation, DNA barcoding
+- name: picrust2_add_descriptions
+  owner: iuc
+  tool_panel_section_label: Phylogenetic reconstruction, Expression analysis, Rarefaction,
+    Pathway analysis
+- name: picrust2_hsp
+  owner: iuc
+  tool_panel_section_label: Phylogenetic reconstruction, Expression analysis, Rarefaction,
+    Pathway analysis
+- name: picrust2_metagenome_pipeline
+  owner: iuc
+  tool_panel_section_label: Phylogenetic reconstruction, Expression analysis, Rarefaction,
+    Pathway analysis
+- name: picrust2_pathway_pipeline
+  owner: iuc
+  tool_panel_section_label: Phylogenetic reconstruction, Expression analysis, Rarefaction,
+    Pathway analysis
+- name: picrust2_pipeline
+  owner: iuc
+  tool_panel_section_label: Phylogenetic reconstruction, Expression analysis, Rarefaction,
+    Pathway analysis
+- name: picrust2_place_seqs
+  owner: iuc
+  tool_panel_section_label: Phylogenetic reconstruction, Expression analysis, Rarefaction,
+    Pathway analysis
+- name: picrust2_shuffle_predictions
+  owner: iuc
+  tool_panel_section_label: Phylogenetic reconstruction, Expression analysis, Rarefaction,
+    Pathway analysis
+- name: PlasFlow
+  owner: iuc
+  tool_panel_section_label: ''
+- name: plasmidfinder
+  owner: iuc
+  tool_panel_section_label: Genome assembly, Scaffolding, Multilocus sequence typing
+- name: prokka
+  owner: crs4
+  tool_panel_section_label: Gene prediction, Coding region prediction, Genome annotation
+- name: proteinortho
+  owner: iuc
+  tool_panel_section_label: Homology-based gene prediction
+- name: proteinortho_grab_proteins
+  owner: iuc
+  tool_panel_section_label: Homology-based gene prediction
+- name: proteinortho_summary
+  owner: iuc
+  tool_panel_section_label: Homology-based gene prediction
+- name: pycoqc
+  owner: iuc
+  tool_panel_section_label: ''
+- name: pygenomeTracks
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_collapse_samples
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_make_otu_table
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_align_seqs
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_alpha_diversity
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_alpha_rarefaction
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_assign_taxonomy
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_beta_diversity
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_beta_diversity_through_plots
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_compare_categories
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_core_diversity
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_count_seqs
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_extract_barcodes
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_filter_alignment
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_filter_fasta
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_filter_otus_from_otu_table
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_filter_samples_from_otu_table
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_filter_taxa_from_otu_table
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_jackknifed_beta_diversity
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_make_emperor
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_make_otu_heatmap
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_make_phylogeny
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_multiple_join_paired_ends
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_multiple_split_libraries_fastq
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_pick_closed_reference_otus
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_pick_open_reference_otus
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_pick_otus
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_pick_rep_set
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_plot_taxa_summary
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_split_libraries
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_split_libraries_fastq
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_summarize_taxa
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_summarize_taxa_through_plots
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_upgma_cluster
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qiime_validate_mapping_file
+  owner: iuc
+  tool_panel_section_label: ''
+- name: qualimap_bamqc
+  owner: iuc
+  tool_panel_section_label: Sequencing quality control
+- name: qualimap_counts
+  owner: iuc
+  tool_panel_section_label: Sequencing quality control
+- name: qualimap_multi_bamqc
+  owner: iuc
+  tool_panel_section_label: Sequencing quality control
+- name: qualimap_rnaseq
+  owner: iuc
+  tool_panel_section_label: Sequencing quality control
+- name: quast
+  owner: iuc
+  tool_panel_section_label: Visualisation, Sequence assembly validation
+- name: quickmerge
+  owner: galaxy-australia
+  tool_panel_section_label: Genome assembly, Scaffolding, De-novo assembly, Genotyping
+- name: raxml
+  owner: iuc
+  tool_panel_section_label: Sequence analysis, Phylogenetic tree analysis
+- name: read_it_and_keep
+  owner: iuc
+  tool_panel_section_label: ''
+- name: recentrifuge
+  owner: iuc
+  tool_panel_section_label: Taxonomic classification, Expression analysis, Cross-assembly
+- name: roary
+  owner: iuc
+  tool_panel_section_label: Genome assembly
+- name: rseqc_FPKM_count
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_RNA_fragment_size
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_RPKM_saturation
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_bam2wig
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_bam_stat
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_clipping_profile
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_deletion_profile
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_geneBody_coverage
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_geneBody_coverage2
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_infer_experiment
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_inner_distance
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_insertion_profile
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_junction_annotation
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_junction_saturation
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_mismatch_profile
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_read_GC
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_read_NVC
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_read_distribution
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_read_duplication
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_read_hexamer
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_read_quality
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: rseqc_tin
+  owner: nilesh
+  tool_panel_section_label: Data handling
+- name: sarscov2formatter
+  owner: iuc
+  tool_panel_section_label: ''
+- name: sarscov2summary
+  owner: iuc
+  tool_panel_section_label: ''
+- name: scoary
+  owner: iuc
+  tool_panel_section_label: ''
+- name: semibin_bin
+  owner: iuc
+  tool_panel_section_label: Sequence assembly, Read binning
+- name: semibin_concatenate_fasta
+  owner: iuc
+  tool_panel_section_label: Sequence assembly, Read binning
+- name: semibin_generate_cannot_links
+  owner: iuc
+  tool_panel_section_label: Sequence assembly, Read binning
+- name: semibin_generate_sequence_features
+  owner: iuc
+  tool_panel_section_label: Sequence assembly, Read binning
+- name: semibin
+  owner: iuc
+  tool_panel_section_label: Sequence assembly, Read binning
+- name: semibin_train
+  owner: iuc
+  tool_panel_section_label: Sequence assembly, Read binning
+- name: seqkit_fx2tab
+  owner: iuc
+  tool_panel_section_label: DNA transcription, Sequence trimming, DNA translation,
+    Sequence conversion
+- name: seqkit_locate
+  owner: iuc
+  tool_panel_section_label: DNA transcription, Sequence trimming, DNA translation,
+    Sequence conversion
+- name: seqkit_stats
+  owner: iuc
+  tool_panel_section_label: DNA transcription, Sequence trimming, DNA translation,
+    Sequence conversion
+- name: shovill
+  owner: iuc
+  tool_panel_section_label: Genome assembly
+- name: smgu_frameshift_deletions_checks
+  owner: iuc
+  tool_panel_section_label: Read pre-processing, Sequence alignment, Genetic variation
+    analysis
+- name: snap
+  owner: iuc
+  tool_panel_section_label: Gene prediction
+- name: snap_training
+  owner: iuc
+  tool_panel_section_label: Gene prediction
+- name: snippy_core
+  owner: iuc
+  tool_panel_section_label: Phylogenetic tree visualisation, Phylogenetic tree generation,
+    Variant calling
+- name: snippy
+  owner: iuc
+  tool_panel_section_label: Phylogenetic tree visualisation, Phylogenetic tree generation,
+    Variant calling
+- name: snippy_clean_full_aln
+  owner: iuc
+  tool_panel_section_label: Phylogenetic tree visualisation, Phylogenetic tree generation,
+    Variant calling
+- name: sonneityping
+  owner: iuc
+  tool_panel_section_label: ''
+- name: spades_biosyntheticspades
+  owner: iuc
+  tool_panel_section_label: ''
+- name: spades_coronaspades
+  owner: iuc
+  tool_panel_section_label: ''
+- name: spades_metaplasmidspades
+  owner: iuc
+  tool_panel_section_label: ''
+- name: metaspades
+  owner: iuc
+  tool_panel_section_label: ''
+- name: spades_metaviralspades
+  owner: iuc
+  tool_panel_section_label: ''
+- name: spades_plasmidspades
+  owner: iuc
+  tool_panel_section_label: ''
+- name: rnaspades
+  owner: iuc
+  tool_panel_section_label: ''
+- name: spades_rnaviralspades
+  owner: iuc
+  tool_panel_section_label: ''
+- name: spades
+  owner: iuc
+  tool_panel_section_label: ''
+- name: spotyping
+  owner: iuc
+  tool_panel_section_label: Variant pattern analysis
+- name: srst2
+  owner: iuc
+  tool_panel_section_label: ''
+- name: structure
+  owner: iuc
+  tool_panel_section_label: Genetic variation analysis
+- name: taxonomy_krona_chart
+  owner: crs4
+  tool_panel_section_label: Visualisation
+- name: tb_profiler_profile
+  owner: iuc
+  tool_panel_section_label: ''
+- name: transtermhp
+  owner: iuc
+  tool_panel_section_label: ''
+- name: unicycler
+  owner: iuc
+  tool_panel_section_label: Genome assembly, Aggregation
+- name: usher_matutils
+  owner: iuc
+  tool_panel_section_label: ''
+- name: usher
+  owner: iuc
+  tool_panel_section_label: ''
+- name: valet
+  owner: iuc
+  tool_panel_section_label: ''
+- name: vapor
+  owner: iuc
+  tool_panel_section_label: Data retrieval, De-novo assembly, Read mapping
+- name: vegan_diversity
+  owner: iuc
+  tool_panel_section_label: ''
+- name: vegan_fisher_alpha
+  owner: iuc
+  tool_panel_section_label: ''
+- name: vegan_rarefaction
+  owner: iuc
+  tool_panel_section_label: ''
+- name: velvetg
+  owner: devteam
+  tool_panel_section_label: Formatting, De-novo assembly
+- name: velveth
+  owner: devteam
+  tool_panel_section_label: Formatting, De-novo assembly
+- name: velvetoptimiser
+  owner: simon-gladman
+  tool_panel_section_label: Optimisation and refinement, Sequence assembly
+- name: vsearch_alignment
+  owner: iuc
+  tool_panel_section_label: DNA mapping, Chimera detection
+- name: vsearch_chimera_detection
+  owner: iuc
+  tool_panel_section_label: DNA mapping, Chimera detection
+- name: vsearch_clustering
+  owner: iuc
+  tool_panel_section_label: DNA mapping, Chimera detection
+- name: vsearch_dereplication
+  owner: iuc
+  tool_panel_section_label: DNA mapping, Chimera detection
+- name: vsearch_masking
+  owner: iuc
+  tool_panel_section_label: DNA mapping, Chimera detection
+- name: vsearch_search
+  owner: iuc
+  tool_panel_section_label: DNA mapping, Chimera detection
+- name: vsearch_shuffling
+  owner: iuc
+  tool_panel_section_label: DNA mapping, Chimera detection
+- name: vsearch_sorting
+  owner: iuc
+  tool_panel_section_label: DNA mapping, Chimera detection
+- name: bamtools
+  owner: devteam
+  tool_panel_section_label: ''
+- name: bacteria_tradis
+  owner: iuc
+  tool_panel_section_label: ''
+- name: tradis_essentiality
+  owner: iuc
+  tool_panel_section_label: ''
+- name: tradis_gene_insert_sites
+  owner: iuc
+  tool_panel_section_label: ''
+- name: kraken-filter
+  owner: devteam
+  tool_panel_section_label: ''
+- name: kraken-mpa-report
+  owner: devteam
+  tool_panel_section_label: ''
+- name: kraken-report
+  owner: devteam
+  tool_panel_section_label: ''
+- name: kraken-translate
+  owner: devteam
+  tool_panel_section_label: ''
+- name: kraken
+  owner: devteam
+  tool_panel_section_label: ''
+- name: kraken2
+  owner: iuc
+  tool_panel_section_label: Taxonomic classification
+- name: eggnog_mapper
+  owner: galaxyp
+  tool_panel_section_label: Homology-based gene prediction, Genome annotation, Fold
+    recognition, Information extraction, Query and retrieval
+- name: eggnog_mapper_annotate
+  owner: galaxyp
+  tool_panel_section_label: Homology-based gene prediction, Genome annotation, Fold
+    recognition, Information extraction, Query and retrieval
+- name: eggnog_mapper_search
+  owner: galaxyp
+  tool_panel_section_label: Homology-based gene prediction, Genome annotation, Fold
+    recognition, Information extraction, Query and retrieval
+- name: metagene_annotator
+  owner: galaxyp
+  tool_panel_section_label: ''
+- name: pampa_communitymetrics
+  owner: ecology
+  tool_panel_section_label: ''
+- name: pampa_presabs
+  owner: ecology
+  tool_panel_section_label: ''
+- name: pampa_glmcomm
+  owner: ecology
+  tool_panel_section_label: ''
+- name: pampa_glmsp
+  owner: ecology
+  tool_panel_section_label: ''
+- name: pampa_plotglm
+  owner: ecology
+  tool_panel_section_label: ''
+- name: obisindicators
+  owner: ecology
+  tool_panel_section_label: ''
+- name: obis_data
+  owner: ecology
+  tool_panel_section_label: ''
diff --git a/results/microgalaxy/tools_filtered_by_ts_categories.tsv b/results/microgalaxy/tools_filtered_by_ts_categories.tsv
new file mode 100644
index 00000000..b802a85f
--- /dev/null
+++ b/results/microgalaxy/tools_filtered_by_ts_categories.tsv
@@ -0,0 +1,857 @@
+Galaxy wrapper id	Total tool usage (usegalaxy.eu)	No. of tool users (2022-2023) (usegalaxy.eu)	Galaxy tool ids	Description	bio.tool id	bio.tool ids	biii	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	https://usegalaxy.org	https://usegalaxy.org.au	https://usegalaxy.eu	https://usegalaxy.fr	Reviewed	To keep
+AggregateAlignments			graphclust_aggregate_alignments	Aggregate and filter alignment metrics of individual clusters, like the output of graphclust_align_cluster.								Up-to-date		RNA	graphclust_aggregate_alignments	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AggregateAlignments	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AggregateAlignments	0.6.0	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+AlignCluster			graphclust_align_cluster	Align predicted clusters of glob_report_no_align step with locarna and conservation analysis and visualizations.								To update		RNA	graphclust_align_cluster	rnateam	https://github.com/bgruening/galaxytools/tools/GraphClust/AlignCluster	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/AlignCluster	0.1	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+CMFinder			cmFinder	Determines consensus motives for sequences.								To update		RNA	graphclust_cmfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CMFinder	0.4	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+CollectResults			glob_report	Post-processing. Redundant clusters are merged and instances that belong to multiple clusters are assigned unambiguously. For every pair of clusters, the relative overlap (i.e. the fraction of instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%. instances that occur in both clusters) is computed and clusters are merged if the overlap exceeds 50%.								To update		RNA	graphclust_postprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResults	0.5	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+CollectResultsNoAlign			graphclust_glob_report_no_align	Redundant GraphClust clusters are merged and instances that belong to multiple clusters are assigned unambiguously.								To update		RNA	graphclust_postprocessing_no_align	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/CollectResultsNoAlign	0.5	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+EMLassemblyline			eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template	Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa								To update	https://github.com/EDIorg/EMLassemblyline	Ecology	emlassemblyline	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline	0.1.1+galaxy0	r-emlassemblyline		(0/9)	(0/9)	(9/9)	(9/9)	True	False
+Ecoregionalization_workflow			ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker	Tools to compute ecoregionalization with BRT model predictions and clustering.								To update	https://github.com/PaulineSGN/Workflow_Galaxy	Ecology	ecoregionalization	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow	0.1.0+galaxy0	r-base		(0/6)	(0/6)	(6/6)	(5/6)	True	False
+GAFA			gafa	Gene Align and Family Aggregator								To update	http://aequatus.tgac.ac.uk	Visualization	gafa	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA	0.3.1			(0/1)	(0/1)	(1/1)	(0/1)	True	False
+GSPAN			gspan	Second step of GraphClust								To update		RNA	graphclust_fasta_to_gspan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/GSPAN	0.4	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+Geom_mean_workflow			Map_shp, Mean_geom, bar_plot	Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France).								To update	https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom	Ecology	Geometric means (Dead wood)	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow	0.1.0+galaxy0	r-base		(0/3)	(0/3)	(3/3)	(3/3)	True	False
+LocARNAGraphClust			locarna_best_subtree	MLocARNA computes a multiple sequence-structure alignment of RNA sequences.								To update		RNA	graphclust_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/LocARNAGraphClust	0.4	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+NSPDK			NSPDK_candidateClust, nspdk_sparse	Produces an explicit sparse feature encoding and copmutes global feature index and returns top dense sets.								To update		RNA	graphclust_nspdk	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/NSPDK	9.2.3.1	graphclust-wrappers	0.6.0	(0/2)	(0/2)	(2/2)	(0/2)	True	False
+PAMPA			pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm	Tools to compute and analyse biodiversity metrics								To update		Ecology	pampa	ecology	https://github.com/ColineRoyaux/PAMPA-Galaxy	https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA	0.0.2			(0/5)	(5/5)	(5/5)	(5/5)	True	True
+Plotting			motifFinderPlot	Plotting results for GraphClust								To update		RNA	graphclust_motif_finder_plot	rnateam	https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Plotting	0.4	seaborn		(0/1)	(0/1)	(1/1)	(0/1)	True	False
+PrepareForMlocarna			preMloc	This tool prepares files for locarna step.								To update		RNA	graphclust_prepocessing_for_mlocarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/PrepareForMlocarna	0.4	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+Preprocessing			preproc	Preprocessing input for GraphClust								To update		RNA	graphclust_preprocessing	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Preprocessing	0.5	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+Structure_GSPAN			structure_to_gspan	Convert RNA structure to GSPAN graphs								To update		RNA	structure_to_gspan	rnateam	https://github.com/mmiladi/galaxytools/blob/graphclust-gspan/tools/GraphClust/Structure_GSPAN	https://github.com/bgruening/galaxytools/tree/master/tools/GraphClust/Structure_GSPAN	0.4	graphclust-wrappers	0.6.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+ThermoRawFileParser			thermo_raw_file_converter	Thermo RAW file converter								To update	https://github.com/compomics/ThermoRawFileParser	Proteomics	thermo_raw_file_converter	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser	1.3.4	thermorawfileparser	1.4.4	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+TreeBest			treebest_best	TreeBeST best	treebest	treebest		TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+TrimNs			trimns	TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline								To update	https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs	Assembly	trimns	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN	https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs	0.1.0	trimns_vgp	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+abacas			abacas	Order and Orientate Contigs								To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23	(0/1)	(0/1)	(0/1)	(1/1)	True	True
+abricate	496717.0	1764.0	abricate, abricate_list, abricate_summary	Mass screening of contigs for antiobiotic resistance genes	ABRicate	ABRicate		ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.	Antimicrobial resistance prediction	Genomics, Microbiology	Up-to-date	https://github.com/tseemann/abricate	Sequence Analysis	abricate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate	1.0.1	abricate	1.0.1	(3/3)	(3/3)	(3/3)	(3/3)	True	True
+abritamr			abritamr	A pipeline for running AMRfinderPlus and collating results into functional classes	abritamr	abritamr		abriTAMR	an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups.	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	To update	https://zenodo.org/record/7370628	Sequence Analysis	abritamr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr	1.0.14	abritamr	1.0.17	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+abyss	4278.0	391.0	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss		ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.7	abyss	2.3.7	(0/1)	(1/1)	(1/1)	(0/1)	True	True
+adapter_removal	217.0	37.0	adapter_removal	Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads.	adapterremoval	adapterremoval		AdapterRemoval	AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available.	Sequence trimming, Sequence merging, Primer removal		Up-to-date	https://github.com/MikkelSchubert/adapterremoval	Fasta Manipulation, Sequence Analysis	adapter_removal	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/adapter_removal/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal	2.3.3	adapterremoval	2.3.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+aegean			aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval	AEGeAn toolkit wrappers	gaeval	gaeval		GAEVAL	Gene Annotation EVAluation.	Sequence annotation	Sequence analysis, Gene structure	Up-to-date	https://github.com/BrendelGroup/AEGeAn	Transcriptomics, Sequence Analysis	aegean	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean	0.16.0	aegean	0.16.0	(1/4)	(4/4)	(4/4)	(4/4)	True	False
+aldex2	129.0	13.0	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2		ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+align_back_trans	329.0	11.0	align_back_trans	Thread nucleotides onto a protein alignment (back-translation)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	Fasta Manipulation, Sequence Analysis	align_back_trans	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans	0.0.10	biopython	1.70	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+amplican	53.0	12.0	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican		amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+ampvis2			ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn	ampvis2	ampvis	ampvis		ampvis	ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.	Analysis, Visualisation	Biodiversity	To update	https://github.com/MadsAlbertsen/ampvis2/	Metagenomics	ampvis2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2	2.8.6			(0/19)	(0/19)	(19/19)	(0/19)	True	False
+amrfinderplus	591.0		amrfinderplus	"""AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms."	amrfinderplus	amrfinderplus		AMRFinderPlus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms"	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	To update	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.11.26	ncbi-amrfinderplus	3.12.8	(0/1)	(0/1)	(1/1)	(1/1)	True	True
+ancombc	7.0	4.0	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc		ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+anndata			anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom	Import, Export, Inspect and Manipulate Anndata and Loom objects								To update	https://anndata.readthedocs.io	Transcriptomics, Sequence Analysis	anndata	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata	0.10.3	anndata	0.6.22.post1	(5/5)	(4/5)	(5/5)	(0/5)	True	False
+annotatemyids	26115.0	1175.0	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	annotatemyids	annotatemyids		annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.	Annotation		Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids	3.18.0	bioconductor-org.hs.eg.db	3.18.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+antarna	52.0	2.0	antarna	antaRNA uses ant colony optimization to solve the inverse folding problem in RNA research .								To update		RNA	antarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/antarna	1.1	antarna	2.0.1.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+antismash	14596.0	279.0	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash		antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	(1/1)	(1/1)	(1/1)	(0/1)	True	True
+aresite2	65.0	4.0	AREsite2_REST	AREsite2 REST Interface								To update	http://rna.tbi.univie.ac.at/AREsite	RNA, Data Source, Sequence Analysis	aresite2	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2	0.1.2	python		(0/1)	(0/1)	(1/1)	(0/1)	True	False
+arriba	3436.0	28.0	arriba, arriba_draw_fusions, arriba_get_filters	Arriba detects fusion genes in RNA-Seq data after running RNA-STAR								Up-to-date	https://github.com/suhrig/arriba	Sequence Analysis, Transcriptomics	arriba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba	https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba	2.4.0	arriba	2.4.0	(0/3)	(3/3)	(3/3)	(0/3)	True	False
+art			art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	art	art		ART	ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD	Conversion	Bioinformatics	To update		Sequence Analysis, Data Source	art	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/art	https://github.com/galaxyproject/tools-iuc/tree/main/tools/art	2014.11.03.0	art	2016.06.05	(0/3)	(0/3)	(0/3)	(0/3)	True	False
+artic			artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic		ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	(0/2)	(0/2)	(2/2)	(0/2)	True	True
+assembly-stats			assembly_stats	Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.								Up-to-date	https://github.com/rjchallis/assembly-stats	Assembly	assembly_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats	17.02	rjchallis-assembly-stats	17.02	(0/1)	(0/1)	(0/1)	(1/1)	True	False
+assemblystats			assemblystats	Summarise an assembly (e.g. N50 metrics)								To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+augustus	8864.0	516.0	augustus	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.								To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	https://github.com/bgruening/galaxytools/tree/master/tools/augustus	3.1.0	augustus	3.5.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+augustus	8864.0	516.0	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	augustus	augustus		AUGUSTUS	AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.	Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation	Gene transcripts, Gene and protein families	To update	http://bioinf.uni-greifswald.de/augustus/	Sequence Analysis	augustus	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus	3.4.0	augustus	3.5.0	(2/2)	(2/2)	(2/2)	(2/2)	True	False
+b2btools			b2btools_single_sequence	This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.	b2btools	b2btools		b2bTools	The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA	Protein disorder prediction, Protein secondary structure prediction, Protein feature detection		To update	https://bio2byte.be	Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools	3.0.5+galaxy0	b2btools	3.0.6	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+bakta	2982.0	151.0	bakta	"""Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."""	Bakta	Bakta		Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	To update	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.2	bakta	1.9.3	(0/1)	(1/1)	(1/1)	(1/1)	True	True
+bam2mappingstats			bam2mappingstats	Generates mapping stats from a bam file.								To update	https://github.com/phac-nml/galaxy_tools	Assembly	bam2mappingstats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bam2mappingstats	1.1.0	perl		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+bamclipper			bamclipper	Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format.								Up-to-date	https://github.com/tommyau/bamclipper	Sequence Analysis	bamclipper	nml	https://github.com/tommyau/bamclipper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/bamclipper	1.0.0	bamclipper	1.0.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+bamhash	169.0	15.0	bamhash	Hash BAM and FASTQ files to verify data integrity								Up-to-date	https://github.com/DecodeGenetics/BamHash	Sequence Analysis	bamhash	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	https://github.com/bgruening/galaxytools/tree/master/tools/bamhash	1.1	bamhash	1.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+bamparse			bamparse	Generates hit count lists from bam alignments.								To update	http://artbio.fr	RNA, Transcriptomics	bamparse	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	https://github.com/ARTbio/tools-artbio/tree/main/tools/bamparse	4.1.1	pysam	0.22.1	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+bamtools	14039.0	208.0	bamtools	Operate on and transform BAM datasets in various ways using bamtools	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools	2.5.2	bamtools	2.5.2	(1/1)	(0/1)	(1/1)	(1/1)	True	True
+bamtools_filter	114845.0	1195.0	bamFilter	Filter BAM datasets on various attributes using bamtools filter	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM	bamtools_filter	devteam	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter	2.5.2	bamtools	2.5.2	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+bamtools_split	1434.0	47.0	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag	Utility for filtering BAM files. It is based on the BAMtools suiteof tools by Derek Barnett.	bamtools	bamtools		BamTools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.	Data handling, Sequence alignment analysis	Sequencing, Data management, Sequence analysis	Up-to-date	https://github.com/pezmaster31/bamtools	Sequence Analysis, SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split	2.5.2	bamtools	2.5.2	(4/4)	(2/4)	(4/4)	(0/4)	True	False
+bamutil			bamutil_clip_overlap, bamutil_diff	bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.								To update	https://github.com/statgen/bamUtil	Sequence Analysis	bamutil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil		bamutil	1.0.15	(1/2)	(1/2)	(1/2)	(0/2)	True	False
+bandage	44390.0	2016.0	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage		Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	(2/2)	(2/2)	(2/2)	(2/2)	True	True
+barcode_collapse			barcode_collapse	Paired End randomer aware duplicate removal algorithm								To update	https://github.com/YeoLab/gscripts	RNA, Sequence Analysis	barcode_collapse	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	https://github.com/bgruening/galaxytools/tree/master/tools/barcode_collapse	0.1.0	pysam	0.22.1	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+baredsc			baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d	baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	baredsc	baredsc		baredSC	The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data.	Data retrieval, Expression correlation analysis, Differential gene expression profiling	RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability	Up-to-date	https://github.com/lldelisle/baredSC	Transcriptomics, Visualization	baredsc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/baredsc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc	1.1.3	baredsc	1.1.3	(4/4)	(0/4)	(4/4)	(0/4)	True	False
+barrnap	3938.0	160.0	barrnap	Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences.	barrnap	barrnap		Barrnap	Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).	Gene prediction	Genomics, Model organisms, Model organisms	To update		Sequence Analysis	barrnap	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap	1.2.2	barrnap	0.9	(0/1)	(1/1)	(1/1)	(1/1)	True	False
+bax2bam	200.0	8.0	bax2bam	BAX to BAM converter								Up-to-date	https://github.com/pacificbiosciences/bax2bam/	Convert Formats, Sequence Analysis	bax2bam	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam	0.0.11	bax2bam	0.0.11	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+bayescan	64.0	8.0	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan		BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+bbtools			bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.								Up-to-date	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.06	bbmap	39.06	(6/6)	(1/6)	(5/6)	(0/6)	True	True
+bctools			bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events	bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0								Up-to-date	https://github.com/dmaticzka/bctools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools	0.2.2	bctools	0.2.2	(0/7)	(0/7)	(7/7)	(0/7)	True	False
+bed_to_protein_map	385.0	49.0	bed_to_protein_map	Converts a BED file to a tabular list of exon locations								To update		Proteomics	bed_to_protein_map	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map	0.2.0	python		(1/1)	(1/1)	(1/1)	(0/1)	True	False
+bellerophon	1194.0	123.0	bellerophon	Filter mapped reads where the mapping spans a junction, retaining the 5-prime read.								Up-to-date	https://github.com/davebx/bellerophon	Sequence Analysis	bellerophon	iuc	https://github.com/davebx/bellerophon	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon	1.0	bellerophon	1.0	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+best_regression_subsets	3.0		BestSubsetsRegression1	Perform Best-subsets Regression								To update		Sequence Analysis, Variant Analysis	best_regression_subsets	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets	https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets	1.0.0	numpy		(1/1)	(0/1)	(1/1)	(1/1)	True	False
+bigscape			bigscape	Construct sequence similarity networks of BGCs and groups them into GCF								Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+binning_refiner	81.0	21.0	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner		Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+biohansel			biohansel	Heidelberg and Enteritidis SNP Elucidation								To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+bioinformatics_cafe			fasta_regex_finder	Miscellanea of scripts for bioinformatics								To update	https://github.com/dariober/bioinformatics-cafe/	Sequence Analysis	bioinformatics_cafe	mbernt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe	0.1.0	python		(1/1)	(0/1)	(1/1)	(0/1)	True	False
+biom_format			biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat		biomformat	"This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods."	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	(2/6)	(2/6)	(6/6)	(0/6)	True	True
+bionano			bionano_scaffold	Bionano Solve is a set of tools for analyzing Bionano data								To update	https://bionanogenomics.com/	Assembly	bionano	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	https://github.com/bgruening/galaxytools/tree/master/tools/bionano	3.7.0			(1/1)	(1/1)	(1/1)	(0/1)	True	False
+bioperl			bp_genbank2gff3	Converts GenBank format files to GFF3	bioperl	bioperl		BioPerl	A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.  It provides software modules for many of the typical tasks of bioinformatics programming.	Data handling, Service invocation	Genomics, Software engineering, Data management	To update	https://bioperl.org/	Sequence Analysis	bp_genbank2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bioperl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl	1.1	perl-bioperl	1.7.8	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+biotradis			bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis		biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	(3/3)	(0/3)	(0/3)	(0/3)	True	True
+biscot	3.0	1.0	biscot	Bionano scaffolding correction tool								Up-to-date	https://github.com/institut-de-genomique/biscot	Assembly	biscot	iuc	https://github.com/bgruening/iuc/tree/master/tools/biscot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot	2.3.3	biscot	2.3.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+bismark	13575.0	404.0	bismark_pretty_report, bismark_bowtie2, bismark_deduplicate, bismark_methylation_extractor	A tool to map bisulfite converted sequence reads and determine cytosine methylation states								To update	https://www.bioinformatics.babraham.ac.uk/projects/bismark/	Sequence Analysis, Next Gen Mappers	bismark	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	https://github.com/bgruening/galaxytools/tree/master/tools/bismark	0.22.1	bismark	0.24.2	(0/4)	(4/4)	(4/4)	(4/4)	True	False
+blast2go	1232.0	101.0	blast2go	Maps BLAST results to GO annotation terms								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe		(0/1)	(0/1)	(0/1)	(0/1)	True	True
+blast_parser	296.0	27.0	blast_parser	Convert 12- or 24-column BLAST output into 3-column hcluster_sg input								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	blast_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser	0.1.2			(0/1)	(0/1)	(1/1)	(0/1)	True	False
+blast_plus_remote_blastp			blast_plus_remote_blastp	NCBI BLAST+ with -remote option								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	blast_plus_remote_blastp	galaxyp	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp	2.6.0	blast	2.15.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+blast_rbh	22499.0	121.0	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+blast_to_scaffold			blast2scaffold	Generate DNA scaffold from blastn or tblastx alignments of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blast_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold	1.1.0	python		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+blastparser_and_hits			BlastParser_and_hits	Parse blast outputs and compile hits								To update	http://artbio.fr	Assembly, RNA	blastparser_and_hits	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/blastparser_and_hits	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastparser_and_hits	2.7.1	python		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+blastx_to_scaffold			blastx2scaffold	Generate DNA scaffold from blastx alignment of Contigs								To update	http://artbio.fr	RNA, Sequence Analysis, Assembly	blastx_to_scaffold	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold	1.1.1	python		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+blastxml_to_gapped_gff3	185.0	24.0	blastxml_to_gapped_gff3	BlastXML to gapped GFF3								To update		Convert Formats, Sequence Analysis	blastxml_to_gapped_gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3	1.1	bcbiogff	0.6.6	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+blastxml_to_top_descr	264558.0	159.0	blastxml_to_top_descr	Make table of top BLAST match descriptions								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	Convert Formats, Sequence Analysis, Text Manipulation	blastxml_to_top_descr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr	0.1.2	python		(0/1)	(0/1)	(1/1)	(0/1)	True	True
+blat_coverage_report			generate_coverage_report	Polymorphism of the Reads								To update		Next Gen Mappers, Sequence Analysis	blat_coverage_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report	1.0.0			(0/1)	(0/1)	(0/1)	(0/1)	True	False
+blat_mapping			blat2wig	Coverage of the Reads in wiggle format								To update		Next Gen Mappers, Sequence Analysis	blat_mapping	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping	https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping	1.0.0			(0/1)	(0/1)	(0/1)	(0/1)	True	False
+blobtoolkit	685.0	21.0	blobtoolkit	Identification and isolation non-target data in draft and publicly available genome assemblies.								To update	https://blobtoolkit.genomehubs.org/	Sequence Analysis, Assembly	blobtoolkit	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit	4.0.7			(0/1)	(1/1)	(1/1)	(0/1)	True	False
+blockbuster	3009.0	34.0	blockbuster	Blockbuster detects blocks of overlapping reads using a gaussian-distribution approach.								To update	http://hoffmann.bioinf.uni-leipzig.de/LIFE/blockbuster.html	RNA, Sequence Analysis	blockbuster	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	https://github.com/bgruening/galaxytools/tree/master/tools/blockbuster	0.1.2	blockbuster	0.0.1.1	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+blockclust	1478.0	15.0	blockclust	BlockClust detects transcripts with similar processing patterns.								Up-to-date	https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust	RNA	blockclust	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust	1.1.1	blockclust	1.1.1	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+bracken	18351.0	326.0	est_abundance	Bayesian Reestimation of Abundance with KrakEN	bracken	bracken		Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	Statistical calculation	Metagenomics, Microbial ecology	Up-to-date	https://ccb.jhu.edu/software/bracken/	Sequence Analysis, Metagenomics	bracken	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken	2.9	bracken	2.9	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+braker	109.0	17.0	braker	BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .								To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	2.1.6			(0/1)	(0/1)	(1/1)	(0/1)	True	False
+braker3	567.0	10.0	braker3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes .	braker3	braker3		BRAKER3	BRAKER3 is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes	Genome annotation, Gene prediction	RNA-Seq, Genomics, Structure prediction, Sequence analysis	To update	https://github.com/Gaius-Augustus/BRAKER	Genome annotation	braker3	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/braker	https://github.com/genouest/galaxy-tools/tree/master/tools/braker3	3.0.8			(0/1)	(1/1)	(1/1)	(1/1)	True	False
+bumbershoot			idpqonvertEmbedder, idpassemble, idpqonvert, idpquery, myrimatch									To update	http://proteowizard.sourceforge.net/	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bumbershoot	3.0.21142	bumbershoot	3_0_21142_0e4f4a4	(0/5)	(0/5)	(5/5)	(0/5)	True	False
+bundle_collections			bundle_collection	Tool to bundle up list collection into a single zip to be download								To update		Sequence Analysis	bundle_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/bundle_collections	1.3.0	perl-getopt-long	2.54	(0/1)	(1/1)	(0/1)	(1/1)	True	False
+busco	86180.0	1804.0	busco	BUSCO assess genome and annotation completeness	busco	busco		BUSCO	Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	To update	https://gitlab.com/ezlab/busco/-/releases	Sequence Analysis	busco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco	5.5.0	busco	5.7.1	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+bwameth	10619.0	201.0	bwameth	Fast and accurate alignment of BS-seq reads								To update	https://github.com/brentp/bwa-meth	Sequence Analysis, Next Gen Mappers	bwameth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth	0.2.6	bwameth	0.2.7	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+cactus			cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	cactus	cactus		Cactus	Cactus is a reference-free whole-genome multiple alignment program.	Multiple sequence alignment, Genome alignment	Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics	To update	https://github.com/ComparativeGenomicsToolkit/cactus	Sequence Analysis	cactus	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus	2.7.1			(0/2)	(2/2)	(2/2)	(1/2)	True	False
+calculate_contrast_threshold			calculate_contrast_threshold	Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.								To update	https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold	Visualization, Genomic Interval Operations, SAM	calculate_contrast_threshold	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold	1.0.0	numpy		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+calisp			calisp	Calgary approach to isotopes in proteomics								Up-to-date	https://github.com/kinestetika/Calisp/	Proteomics	calisp	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/calisp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/calisp	3.0.13	calisp	3.0.13	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+cap3	7766.0	101.0	cap3	cap3 wrapper								To update	http://artbio.fr	Assembly	cap3	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	https://github.com/ARTbio/tools-artbio/tree/main/tools/cap3	2.0.1	cap3	10.2011	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+cardinal			cardinal_classification, cardinal_colocalization, cardinal_combine, cardinal_data_exporter, cardinal_filtering, cardinal_mz_images, cardinal_preprocessing, cardinal_quality_report, cardinal_segmentations, cardinal_single_ion_segmentation, cardinal_spectra_plots	Statistical and computational tools for analyzing mass spectrometry imaging datasets								To update	http://cardinalmsi.org	Proteomics, Metabolomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal	2.10.0	bioconductor-cardinal	3.4.3	(0/11)	(9/11)	(11/11)	(11/11)	True	False
+cat			cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)	cat_bins	cat_bins		CAT and BAT	Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs.	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat	5.2.3	cat	5.3	(5/5)	(2/5)	(5/5)	(0/5)	True	True
+cd_hit_dup			cd_hit_dup	simple tool for removing duplicates from sequencing reads								To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1	(1/1)	(0/1)	(0/1)	(0/1)	True	True
+cdhit	8278.0	6.0	cd_hit	Cluster or compare biological sequence datasets	cd-hit	cd-hit		cd-hit	Cluster a nucleotide dataset into representative sequences.	Sequence clustering	Sequencing	Up-to-date	http://weizhongli-lab.org/cd-hit/	Sequence Analysis, Fasta Manipulation	cd_hit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit	4.8.1	cd-hit	4.8.1	(0/1)	(0/1)	(1/1)	(1/1)	True	True
+cell-types-analysis			ct_build_cell_ontology_dict, ct_check_labels, ct_combine_tool_outputs, ct_downsample_cells, ct_get_consensus_outputs, ct_get_empirical_dist, ct_get_tool_perf_table, ct_get_tool_pvals	Tools for analysis of predictions from scRNAseq cell type classification tools, see https://github.com/ebi-gene-expression-group/cell-types-analysis								To update		Transcriptomics, RNA, Statistics	suite_cell_types_analysis	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/cell-types-analysis	1.1.1	cell-types-analysis	0.1.11	(0/8)	(0/8)	(6/8)	(0/8)	True	False
+cemitool	98.0	9.0	cemitool	Gene co-expression network analysis tool	cemitool	cemitool		CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	To update	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.18.1	bioconductor-cemitool	1.26.0	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+champ_blocs			cb_dissim, cb_ivr, cb_div	Compute indicators for turnover boulders fields								To update		Ecology		ecology	https://github.com/Marie59/champ_blocs	https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs	0.0.0	r-base		(0/3)	(0/3)	(3/3)	(3/3)	True	False
+charts	3589.0	287.0	charts	Enables advanced visualization options in Galaxy Charts								To update		Visualization	charts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts	1.0.1	r-getopt		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+checkm			checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm		CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	To update	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.0	checkm-genome	1.2.2	(0/10)	(0/10)	(10/10)	(10/10)	True	True
+cherri			cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	cherri	cherri		cherri	CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions.		Molecular interactions, pathways and networks, Structure analysis, Machine learning	To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri	0.7	cherri	0.8	(0/2)	(0/2)	(2/2)	(0/2)	True	False
+chipseeker	15690.0	418.0	chipseeker	A tool for ChIP peak annotation and visualization								To update	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html	ChIP-seq, Genome annotation	chipseeker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker	1.32.0	bioconductor-chipseeker	1.38.0	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+chira	74.0		chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	chira	chira		ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA	Up-to-date	https://github.com/pavanvidem/chira	RNA, Transcriptomics, Sequence Analysis	chira	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira	1.4.3	chira	1.4.3	(5/5)	(0/5)	(5/5)	(0/5)	True	False
+chromeister	2130.0	182.0	chromeister	ultra-fast pairwise genome comparisons								Up-to-date	https://github.com/estebanpw/chromeister	Sequence Analysis	chromeister	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chromeister	https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister	1.5.a	chromeister	1.5.a	(0/1)	(1/1)	(1/1)	(1/1)	True	False
+chromosome_diagram			chromosome_diagram	Chromosome Diagrams using Biopython								To update		Graphics, Sequence Analysis, Visualization	chromosome_diagram	peterjc		https://github.com/peterjc/pico_galaxy/tree/master/tools/chromosome_diagram	0.0.3	biopython	1.70	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+circexplorer	251.0	8.0	circexplorer	A combined strategy to identify circular RNAs (circRNAs and ciRNAs)								To update	https://github.com/YangLab/CIRCexplorer	Sequence Analysis, RNA	circexplorer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	https://github.com/bgruening/galaxytools/tree/master/tools/circexplorer	1.1.9.0	circexplorer	1.1.10	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+circexplorer2	269.0	16.0	circexplorer2	Comprehensive and integrative circular RNA analysis toolset.	circexplorer2	circexplorer2		CIRCexplorer2	Genome-wide annotation of circRNAs and their alternative back-splicing/splicing.		RNA splicing, Gene transcripts, Literature and language	Up-to-date	https://github.com/YangLab/CIRCexplorer2	RNA, Assembly	circexplorer2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2	2.3.8	circexplorer2	2.3.8	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+clair3	1856.0	68.0	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3		Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	0.1.12	clair3	1.0.8	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+clc_assembly_cell			clc_assembler, clc_mapper	Galaxy wrapper for the CLC Assembly Cell suite from CLCBio								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	Assembly, Next Gen Mappers, SAM	clc_assembly_cell	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	https://github.com/peterjc/pico_galaxy/tree/master/tools/clc_assembly_cell	0.0.7	samtools	1.20	(0/2)	(0/2)	(0/2)	(0/2)	True	False
+climate-stripes			climate_stripes	Create climate stripes from a tabular input file								To update	https://www.climate-lab-book.ac.uk/2018/warming-stripes/	Climate Analysis, Visualization	climate_stripes	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes	1.0.2	python		(1/1)	(1/1)	(1/1)	(0/1)	True	False
+clinod			clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod		clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	(1/1)	(0/1)	(0/1)	(0/1)	True	True
+clustalw	46793.0	651.0	clustalw	ClustalW multiple sequence alignment program for DNA or proteins	clustal2	clustal2		Clustal 2 (Clustal W, Clustal X)	Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2.	Multiple sequence alignment	Phylogeny, Sequence analysis	Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw	2.1	clustalw	2.1	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+cmsearch_deoverlap	102.0	1.0	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap		cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		(0/1)	(0/1)	(1/1)	(0/1)	True	True
+cmv	70.0	1.0	cmcv, cmv, hmmcv, hmmv	cmv is a collection of tools for the visualisation of Hidden Markov Models and RNA-family models.								Up-to-date	https://github.com/eggzilla/cmv	RNA	cmv	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmv	1.0.8	cmv	1.0.8	(0/4)	(0/4)	(2/4)	(0/4)	True	False
+codeml	60901.0	29.0	codeml	Detects positive selection	paml	paml		PAML	Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.	Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml	4.9	paml	4.10.7	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+cofold	342.0	8.0	cofold	Cofold predicts RNA secondary structures that takes co-transcriptional folding into account.								To update	http://www.e-rna.org/cofold/	RNA	cofold	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cofold	2.0.4.0	cofold	2.0.4	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+cojac			cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac		COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.1	cojac	0.9.1	(2/3)	(0/3)	(3/3)	(0/3)	True	True
+colabfold			colabfold_alphafold, colabfold_msa	Protein prediction based on AlphaFold2	Colabfold	Colabfold		ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.	Database search, Protein structure prediction, Fold recognition	Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics	To update	https://github.com/sokrypton/ColabFold	Proteomics, Graphics	colabfold	iuc	https://github.com/sokrypton/ColabFold	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold	1.5.5			(2/2)	(0/2)	(0/2)	(0/2)	True	False
+colibread			commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak	Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome								To update	https://colibread.inria.fr/	Sequence Analysis, Variant Analysis	colibread	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread	24.7.14+galaxy0	commet	24.7.14	(0/7)	(0/7)	(1/7)	(1/7)	True	False
+collapse_collection			collapse_dataset	Collection tool that collapses a list of files into a single datasset in order of appears in collection								To update		Sequence Analysis	collapse_collections	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/collapse_collection	5.1.0	gawk		(1/1)	(1/1)	(1/1)	(1/1)	True	False
+combineJSON			combine_json	JSON collection tool that takes multiple JSON data arrays and combines them into a single JSON array.								To update		Sequence Analysis	combine_json	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combineJSON	0.1			(0/1)	(0/1)	(0/1)	(0/1)	True	False
+combine_assembly_stats			combine_stats	Combine multiple Assemblystats datasets into a single tabular report								To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.54	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+combine_metaphlan_humann			combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann		Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		(0/1)	(0/1)	(1/1)	(0/1)	True	True
+combine_tabular_collection			combine	Combine Tabular Collection into a single file								To update		Sequence Analysis	combine_tabular_collection	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_tabular_collection	0.1			(0/1)	(0/1)	(0/1)	(0/1)	True	False
+compalignp	220.0		compalignp	Compute fractional identity between trusted alignment and test alignment								Up-to-date		RNA, Sequence Analysis	compalignp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp	1.0	compalignp	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+compare_humann2_output	332.0	10.0	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs		Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			(0/1)	(0/1)	(0/1)	(0/1)	True	True
+compleasm			compleasm	Compleasm: a faster and more accurate reimplementation of BUSCO	compleasm	compleasm		compleasm	"""Compleasm: a faster and more accurate reimplementation of BUSCO"""	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Genomics, Transcriptomics, Sequence analysis	Up-to-date	https://github.com/huangnengCSU/compleasm	Sequence Analysis	compleasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm	0.2.6	compleasm	0.2.6	(0/1)	(0/1)	(1/1)	(1/1)	True	True
+compute_motif_frequencies_for_all_motifs	94.0	2.0	compute_motif_frequencies_for_all_motifs	Compute Motif Frequencies For All Motifs, motif by motif.								To update		Sequence Analysis, Statistics	compute_motif_frequencies_for_all_motifs	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motif_frequencies_for_all_motifs	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motif_frequencies_for_all_motifs	1.0.0			(0/1)	(1/1)	(1/1)	(0/1)	True	False
+compute_motifs_frequency	65.0		compute_motifs_frequency	Compute Motif Frequencies in indel flanking regions.								To update		Sequence Analysis, Statistics	compute_motifs_frequency	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/compute_motifs_frequency	https://github.com/galaxyproject/tools-devteam/tree/main/tools/compute_motifs_frequency	1.0.0			(0/1)	(1/1)	(1/1)	(0/1)	True	False
+concoct	250.0	29.0	concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering	CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs.	concoct	concoct		CONCOCT	A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.	Sequence clustering, Read binning	Metagenomics	Up-to-date	https://github.com/BinPro/CONCOCT	Metagenomics	concoct	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct	https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct	1.1.0	concoct	1.1.0	(0/5)	(0/5)	(5/5)	(5/5)	True	True
+consensus_from_alignments			aligned_to_consensus	Tool to compute a consensus sequence from several aligned fasta sequences								To update		Sequence Analysis	consalign	ecology	https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments	https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments	1.0.0	r-bioseq		(0/1)	(0/1)	(1/1)	(1/1)	True	False
+consolidate_vcfs			consolidate_vcfs	Combines freebayes and mpileup files for use by vcf2snvalignment								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	consolidate_vcfs	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/consolidate_vcfs	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+coprarna			coprarna	Target prediction for prokaryotic trans-acting small RNAs								To update	https://github.com/PatrickRWright/CopraRNA	RNA, Sequence Analysis	coprarna	rnateam	https://github.com/PatrickRWright/CopraRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/coprarna	2.1.1	coprarna	2.1.4	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+count_gff_features	271.0	49.0	count_gff_features	Count GFF Features								To update		Sequence Analysis	count_gff_features	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/count_gff_features	https://github.com/galaxyproject/tools-devteam/tree/main/tools/count_gff_features	0.2	galaxy-ops	1.1.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+count_roi_variants			count_roi_variants	Count sequence variants in region of interest in BAM file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	Assembly, SAM	count_roi_variants	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants	0.0.6	samtools	1.20	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+coverage_report			CoverageReport2	Generate Detailed Coverage Report from BAM file								To update	https://github.com/galaxyproject/tools-iuc	Sequence Analysis	coverage_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report	0.0.4	perl-number-format	1.76	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+coverage_stats			coverage_stats	BAM coverage statistics using samtools idxstats and depth								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	Assembly, SAM	coverage_stats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	https://github.com/peterjc/pico_galaxy/tree/master/tools/coverage_stats	0.1.0	samtools	1.20	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+coverm			coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm		CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	(0/2)	(0/2)	(2/2)	(2/2)	True	True
+crispr_studio	636.0	30.0	crispr_studio	CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization.	crisprstudio	crisprstudio		CRISPRStudio	CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor.	Visualisation	Sequence analysis, Genomics, Data visualisation	To update	https://github.com/moineaulab/CRISPRStudio	Sequence Analysis	crispr_studio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crispr_studio/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio	1+galaxy0	crispr_studio	1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+crosscontamination_barcode_filter	347.0	17.0	crosscontamination_barcode_filter	Barcode contamination discovery tool								To update		Transcriptomics, Visualization	crosscontamination_barcode_filter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter	0.3	r-ggplot2	2.2.1	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+crt			crispr_recognition_tool	CRISPR Recognition Tool								To update		Sequence Analysis	crispr_recognition_tool	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/crt	https://github.com/bgruening/galaxytools/tree/master/tools/crt	1.2.0	crisper_recognition_tool	1.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+cryptogenotyper	8518.0	16.0	CryptoGenotyper	CryptoGenotyper is a standalone tool to *in-silico*  determine species and subtype based on SSU rRNA and gp60 markers.								Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+ctd_batch	203.0	13.0	ctdBatch_1	CTD analysis of chemicals, diseases, or genes								To update		Sequence Analysis	ctd_batch	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/ctd_batch	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ctd_batch	1.0.0			(0/1)	(0/1)	(1/1)	(0/1)	True	False
+cummerbund	1782.0	31.0	cummeRbund	Wrapper for the Bioconductor cummeRbund library								To update	https://bioconductor.org/packages/release/bioc/html/cummeRbund.html	RNA, Visualization	cummerbund	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cummerbund	2.16.0	fonts-conda-ecosystem		(1/1)	(1/1)	(1/1)	(0/1)	True	False
+custom_pro_db	1652.0	57.0	custom_pro_db	CustomProDB								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db	1.22.0	bioconductor-rgalaxy	1.37.1	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+custom_pro_db_annotation_data_manager				CustomProDB Annotation								To update	https://bioconductor.org/packages/release/bioc/html/customProDB.html	Proteomics	custom_pro_db_annotation_data_manager	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/custom_pro_db_annotation_data_manager				(0/1)	(0/1)	(0/1)	(0/1)	True	False
+cutadapt	232004.0	5090.0	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt		Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.8	cutadapt	4.8	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+dada2			dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2		dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	(10/10)	(10/10)	(10/10)	(10/10)	True	True
+das_tool	550.0	17.0	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool		dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	(0/2)	(0/2)	(2/2)	(2/2)	True	True
+data-hca			hca_matrix_downloader	Tools for interacting with the Human Cell Atlas resource https://prod.data.humancellatlas.org/explore/projects								To update		Transcriptomics, Sequence Analysis	suite_human_cell_atlas_tools	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/data-hca	v0.0.4+galaxy0	hca-matrix-downloader	0.0.4	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+data-scxa			retrieve_scxa	Tools for interacting with the EMBL-EBI Expression Atlas resource https://www.ebi.ac.uk/gxa/home https://www.ebi.ac.uk/gxa/sc/home								To update		Transcriptomics, Sequence Analysis	suite_ebi_expression_atlas	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/data-scxa	v0.0.2+galaxy2	wget		(1/1)	(1/1)	(1/1)	(0/1)	True	False
+data_exploration			tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs	Explore data through multiple statistical tools								To update		Ecology		ecology	https://github.com/Marie59/Data_explo_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration	0.0.0	r-tangles		(0/6)	(0/6)	(6/6)	(6/6)	True	False
+data_manager_eggnog_mapper	9.0	2.0		downloads eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper				(0/1)	(0/1)	(0/1)	(0/1)	True	False
+data_manager_eggnog_mapper_abspath	1.0			download eggnog data for eggnog-mapper								To update		Proteomics	data_manager_eggnog_mapper_abspath	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath				(0/1)	(0/1)	(0/1)	(0/1)	True	False
+dbbuilder	4758.0	161.0	dbbuilder	Protein Database Downloader								To update	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	Proteomics	dbbuilder	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dbbuilder	0.3.4	wget		(0/1)	(1/1)	(1/1)	(1/1)	True	False
+decoyfasta	104.0	15.0		Galaxy tool wrapper for the transproteomic pipeline decoyFASTA tool.								To update		Proteomics	decoyfasta	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/decoyfasta				(0/1)	(0/1)	(0/1)	(0/1)	True	False
+deepsig	5.0		deepsig	Predictor of signal peptides in proteins based on deep learning								Up-to-date	https://github.com/BolognaBiocomp/deepsig	Genome annotation	deepsig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig	1.2.5	deepsig	1.2.5	(0/1)	(0/1)	(1/1)	(1/1)	True	False
+delete_overlapping_indels	39.0	2.0	delete_overlapping_indels	Delete Overlapping Indels from a chromosome indels file								To update		Sequence Analysis	delete_overlapping_indels	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/delete_overlapping_indels	https://github.com/galaxyproject/tools-devteam/tree/main/tools/delete_overlapping_indels	1.0.0			(0/1)	(0/1)	(1/1)	(0/1)	True	False
+deseq2	95752.0	4990.0	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2		DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+deseq2_normalization			deseq2_normalization	Normalizes gene hitlists								To update	http://artbio.fr	RNA, Transcriptomics, Sequence Analysis, Statistics	deseq2_normalization	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	https://github.com/ARTbio/tools-artbio/tree/main/tools/deseq2_normalization	1.40.2+galaxy0	bioconductor-deseq2	1.42.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+dewseq	72.0	11.0	dewseq	DEWSeq is a sliding window based peak caller for eCLIP/iCLIP data								To update	https://github.com/EMBL-Hentze-group/DEWSeq_analysis_helpers	Sequence Analysis, RNA, CLIP-seq	dewseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dewseq	0.1.0+galaxy0	python		(0/1)	(0/1)	(1/1)	(0/1)	True	False
+dexseq	16064.0	218.0	dexseq, dexseq_count, plotdexseq	Inference of differential exon usage in RNA-Seq	dexseq	dexseq		DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.	Enrichment analysis, Exonic splicing enhancer prediction	RNA-Seq	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html	Transcriptomics, RNA, Statistics	dexseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq	1.48.0	bioconductor-dexseq	1.48.0	(3/3)	(3/3)	(3/3)	(3/3)	True	False
+dia_umpire	33.0	2.0	dia_umpire_se	DIA-Umpire analysis for data independent acquisition (DIA) mass spectrometry-based proteomics								To update	http://diaumpire.sourceforge.net/	Proteomics	dia_umpire	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dia_umpire	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dia_umpire	2.1.3	dia_umpire	2.1.6	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+dialignr	40.0	1.0	dialignr	DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks.								To update	https://github.com/shubham1637/DIAlignR	Proteomics	dialignr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/dialignr	1.2.0	bioconductor-dialignr	2.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+diamond	49711.0	963.0	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond		Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	(3/3)	(3/3)	(3/3)	(3/3)	True	True
+diann	15.0	3.0	diann	DiaNN (DIA-based Neural Networks) is a software for DIA/SWATH data processing.								To update	https://github.com/vdemichev/DiaNN	Proteomics	diann	galaxyp	https://github.com/vdemichev/DiaNN	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diann	1.8.1			(0/1)	(1/1)	(1/1)	(0/1)	True	False
+diapysef	245.0	11.0	diapysef	diapysef is a convenience package for working with DIA-PASEF data								To update	https://pypi.org/project/diapysef/	Proteomics	diapysef	galaxyp	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diapysef	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diapysef	0.3.5.0	diapysef	1.0.10	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+diffacto	7.0	5.0	diffacto	Diffacto comparative protein abundance estimation								To update	https://github.com/statisticalbiotechnology/diffacto	Proteomics	diffacto	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/diffacto	1.0.6	diffacto	1.0.7	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+disco	369.0	42.0	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco		DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+divide_pg_snp	31.0		dividePgSnp	Separate pgSnp alleles into columns								To update		Sequence Analysis	divide_pg_snp	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/divide_pg_snp	https://github.com/galaxyproject/tools-devteam/tree/main/tools/divide_pg_snp	1.0.0			(1/1)	(0/1)	(1/1)	(0/1)	True	False
+dorina	1086.0	1.0	dorina_search	data source for RNA interactions in post-transcriptional regulation								To update		RNA, Data Source	dorina	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dorina	1.0			(0/1)	(0/1)	(1/1)	(0/1)	True	False
+dot2ct			rnastructure_dot2ct	Dot-Bracket to Connect Table (CT)								To update		Sequence Analysis, RNA	dot2ct	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct	5.7.a	rnastructure	6.4	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+dotknot	83.0	1.0	dotknot	DotKnot is a heuristic method for pseudoknot prediction in a given RNA sequence								To update	http://dotknot.csse.uwa.edu.au/	RNA, Proteomics	dotknot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna/dotknot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dotknot	1.3.1	vienna_rna		(0/1)	(0/1)	(1/1)	(0/1)	True	False
+dram			dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram		DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	To update	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.3.5	dram	1.5.0	(0/5)	(0/5)	(5/5)	(0/5)	True	True
+drep			drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep		dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	To update	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.4.5	drep	3.5.0	(0/2)	(0/2)	(2/2)	(2/2)	True	True
+droplet-barcode-plot			_dropletBarcodePlot	Make a cell barcode plot for droplet single-cell RNA-seq QC								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	droplet_barcode_plot	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-rank-plot/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/droplet-barcode-plot	1.6.1+galaxy2	scxa-plots	0.0.1	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+dropletutils	3934.0	126.0	dropletutils_empty_drops, dropletutils_read_10x	De-composed DropletUtils functionality tools, based on https://github.com/ebi-gene-expression-group/dropletutils-scripts and DropletUtils 1.0.3								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_dropletutils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/dropletutils	1.0.4	dropletutils-scripts	0.0.5	(2/2)	(0/2)	(2/2)	(0/2)	True	False
+dropletutils	3934.0	126.0	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	dropletutils	dropletutils		DropletUtils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.	Loading, Community profiling	Gene expression, RNA-seq, Sequencing, Transcriptomics	To update	https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html	Transcriptomics, Sequence Analysis	dropletutils	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils	1.10.0	bioconductor-dropletutils	1.22.0	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+ectyper	9907.0	53.0	ectyper	EC-Typer - in silico serotyping of Escherichia coli species								Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+edger	18522.0	945.0	edger	Perform RNA-Seq differential expression analysis using edgeR pipeline	edger	edger		edgeR	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.	Differential gene expression analysis	Genetics, RNA-Seq, ChIP-seq	To update	http://bioconductor.org/packages/release/bioc/html/edgeR.html	Transcriptomics, RNA, Statistics	edger	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger	https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger	3.36.0	bioconductor-edger	4.0.16	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+effectiveT3			effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3		EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+eggnog_mapper	30565.0	510.0	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2		eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	(3/3)	(3/3)	(3/3)	(3/3)	True	True
+egsea	2524.0	177.0	egsea	This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing	egsea	egsea		EGSEA	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.	Gene set testing	Systems biology	To update	https://bioconductor.org/packages/release/bioc/html/EGSEA.html	Transcriptomics, RNA, Statistics	egsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea	1.20.0	bioconductor-egsea	1.28.0	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+emboss_5	89530.0	1816.0	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss		EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	(107/107)	(107/107)	(107/107)	(107/107)	True	True
+encyclopedia			encyclopedia_encyclopedia, encyclopedia_fasta_to_prosit_csv, encyclopedia_library_to_blib, encyclopedia_prosit_csv_to_library, encyclopedia_quantify, encyclopedia_searchtolib, encyclopedia_walnut	Mass Spec Data-Independent Acquisition (DIA) MS/MS analysis								To update	https://bitbucket.org/searleb/encyclopedia/wiki/Home	Proteomics	encyclopedia	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/encyclopedia/tools/encyclopedia	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/encyclopedia	1.12.34	encyclopedia	2.12.30	(2/7)	(4/7)	(7/7)	(0/7)	True	False
+ete	1255.0	67.0	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete		ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	(0/7)	(0/7)	(7/7)	(7/7)	True	True
+exomedepth	410.0	29.0	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	exomedepth	exomedepth		ExomeDepth	Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.	Sequence analysis, Variant calling, Genotyping, Copy number estimation	Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases	To update	https://cran.r-project.org/package=ExomeDepth	Sequence Analysis, Variant Analysis	exomedepth	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exomedepth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth	1.1.0	r-exomedepth	1.1.16	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+exonerate	988.0	59.0	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	exonerate	exonerate		Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.	Pairwise sequence alignment, Protein threading, Genome alignment	Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks	Up-to-date	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate	Sequence Analysis	exonerate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/exonerate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate	2.4.0	exonerate	2.4.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+exparna			exparna	ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules.								Up-to-date	http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp	RNA	exparna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/exparna	1.0.1	exparna	1.0.1	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+export2graphlan	5265.0	200.0	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan		export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+express	325.0	12.0	express	Quantify the abundances of a set of target sequences from sampled subsequences								To update		RNA	express	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/express	https://github.com/galaxyproject/tools-devteam/tree/main/tools/express	1.1.1	eXpress	1.5.1	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+ez_histograms			ez_histograms	ggplot2 histograms and density plots								To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+fargene	459.0	52.0	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene		fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+fasta2bed			fasta2bed	Convert multiple fasta file into tabular bed file format								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fasta2bed	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta2bed	1.0.0	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+fasta_extract	10.0		fa-extract-sequence	extract single fasta from multiple fasta file								To update	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	Sequence Analysis	fasta_extract	nml	https://toolshed.g2.bx.psu.edu/view/nml/fasta_extract	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fasta_extract	1.1.0	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+fasta_filter_by_id			fasta_filter_by_id	Filter FASTA sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	fasta_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fasta_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+fasta_nucleotide_color_plot	322.0	39.0	fasta_nucleotide_color_plot	Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color.								To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot	Visualization	fasta_nucleotide_color_plot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot	1.0.1	openjdk		(1/1)	(0/1)	(1/1)	(0/1)	True	False
+fasta_stats	35332.0	1080.0	fasta-stats	Display summary statistics for a fasta file.								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	Sequence Analysis	fasta_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats	2.0	numpy		(1/1)	(1/1)	(1/1)	(1/1)	True	False
+fastani	3498.0	250.0	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity								To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	(0/1)	(0/1)	(1/1)	(1/1)	True	True
+fastg2protlib	28.0	1.0	fastg2protlib-peptides, fastg2protlib-validate	Generate FASTA from FASTG								To update	https://github.com/galaxyproteomics/fastg2protlib.git	Proteomics	fastg2protlib	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib	1.0.2			(0/2)	(0/2)	(2/2)	(0/2)	True	False
+fastk			fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)								To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+fastp	1055760.0	2803.0	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp		fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+fastq_filter_by_id			fastq_filter_by_id	Filter FASTQ sequences by ID (DEPRECATED)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	Fastq Manipulation, Sequence Analysis, Text Manipulation	fastq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_filter_by_id	0.0.7	galaxy_sequence_utils	1.1.5	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+fastq_pair_names			fastq_pair_names	Extract FASTQ paired read names								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	Sequence Analysis	fastq_pair_names	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names	0.0.5	galaxy_sequence_utils	1.1.5	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+fastq_paired_unpaired			fastq_paired_unpaired	Divide FASTQ file into paired and unpaired reads								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	Sequence Analysis, Text Manipulation	fastq_paired_unpaired	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_paired_unpaired	0.1.5	galaxy_sequence_utils	1.1.5	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+fastq_provider			fastq_provider	Retrieval and download of FASTQ files from ENA and other repositories such as HCA.								To update	https://github.com/ebi-gene-expression-group/atlas-fastq-provider	Data Source, RNA, Transcriptomics	atlas_fastq_provider	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/fastq_provider	0.4.4	atlas-fastq-provider	0.4.7	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+fastq_utils			fastq_filter_n, fastq_trim_poly_at	Set of tools for handling fastq files								To update	https://github.com/nunofonseca/fastq_utils	Transcriptomics, RNA	fastq_utils	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/qc/fastq_utils	0.25.1+galaxy0	fastq_utils	0.25.2	(0/2)	(0/2)	(0/2)	(0/2)	True	False
+fastqc_stats			FastQC_Summary	Summary multiple FastQC into a single tabular line report								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	fastqc_stats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/fastqc_stats	1.2	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+fastqe	4333.0	1266.0	fastqe	FASTQE	fastqe	fastqe		FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+fasttree	55434.0	379.0	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree		FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+feature_alignment	18.0	1.0	feature_alignment	TRIC integrates information from all available runs via a graph-based alignment strategy								Up-to-date		Proteomics	feature_alignment	galaxyp	https://github.com/msproteomicstools/msproteomicstools/blob/master/TRIC-README.md	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment	0.11.0	msproteomicstools	0.11.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+featurecounter	22384.0	6.0	featureCoverage1	Feature coverage								To update		Sequence Analysis, Variant Analysis	featurecounter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/featurecounter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/featurecounter	2.0.0	bx-python	0.11.0	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+featurecounts	696399.0	4679.0	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts		FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+feelnc	1191.0	46.0	feelnc	Galaxy wrapper for FEELnc	feelnc	feelnc		FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.	Annotation, Classification	RNA-seq, Functional, regulatory and non-coding RNA	To update	https://github.com/tderrien/FEELnc	Sequence Analysis	feelnc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc	0.2.1	feelnc	0.2	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+feht			feht	Automatically identify makers predictive of groups.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	feht	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/feht	0.1.0	feht	1.1.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+fermikit			fermi2, fermikit_variants	FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.								Up-to-date	https://github.com/lh3/fermikit	Assembly, Variant Analysis	fermikit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit	r193	fermi2	r193	(0/2)	(0/2)	(0/2)	(0/2)	True	False
+fgsea	5240.0	307.0	fgsea	Perform gene set testing using fgsea	fgsea	fgsea		fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.	Gene-set enrichment analysis	Genetics	To update	https://bioconductor.org/packages/release/bioc/html/fgsea.html	Visualization, Transcriptomics, Statistics	fgsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fgsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea	1.8.0+galaxy1	bioconductor-fgsea	1.28.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+filter_by_fasta_ids	26274.0	426.0	filter_by_fasta_ids	Filter FASTA on the headers and/or the sequences								To update		Fasta Manipulation, Proteomics	filter_by_fasta_ids	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/filter_by_fasta_ids	2.3	python		(1/1)	(1/1)	(1/1)	(1/1)	True	False
+filter_density			filterdensity	Filter out position based on distance between SNVs								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_density	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_density	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+filter_spades_repeats			filter_spades_repeat	Remove short and repeat contigs/scaffolds								To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+filter_stats			filterstat	SNVPhyl filter_stats								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_stats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_stats	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+filter_transcripts_via_tracking	20.0	1.0	filter_combined_via_tracking	Filter Combined Transcripts								To update		RNA	filter_transcripts_via_tracking	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/filter_transcripts_via_tracking	https://github.com/galaxyproject/tools-devteam/tree/main/tools/filter_transcripts_via_tracking	0.1			(1/1)	(1/1)	(1/1)	(1/1)	True	False
+filter_vcf			filtervcf	SNVPhyl filter_vcf								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	filter_vcf	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/filter_vcf	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+filtlong	30483.0	617.0	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong		Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+find_diag_hits	69.0	5.0	find_diag_hits	Find diagnostic hits								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	find_diag_hits	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/find_diag_hits	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/find_diag_hits	1.0.0	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+find_repeats			findrepeat	Find repetitive regions on a reference genome using MUMMer								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	find_repeats	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/find_repeats	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+fisher_test			fishertest	Fisher's exact test on two-column hit lists.								To update	http://artbio.fr	RNA, Statistics	fishertest	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	https://github.com/ARTbio/tools-artbio/tree/main/tools/fisher_test	2.32.0+galaxy0	bioconductor-qvalue	2.34.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+flair			flair_collapse, flair_correct	FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads.								To update	https://github.com/BrooksLabUCSC/flair	Nanopore	flair	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flair	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair	1.5	flair	2.0.0	(0/2)	(0/2)	(2/2)	(0/2)	True	False
+flash	13759.0	74.0	flash	Fast Length Adjustment of SHort reads	flash	flash		FLASH	Identifies paired-end reads which overlap in the middle, converting them to single long reads	Read pre-processing, Sequence merging, Sequence assembly	Sequencing, Sequence assembly	Up-to-date	https://ccb.jhu.edu/software/FLASH/	Assembly, Fastq Manipulation	flash	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash	1.2.11	flash	1.2.11	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+flashlfq	645.0	17.0	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq		FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	(0/1)	(1/1)	(1/1)	(0/1)	True	True
+flye	20904.0	1499.0	flye	Assembly of long and error-prone reads.	Flye	Flye		Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.3	flye	2.9.3	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+format_metaphlan2_output	5588.0	166.0	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output		Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			(0/1)	(0/1)	(1/1)	(0/1)	True	True
+fraggenescan	1102.0	68.0	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan		FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	(0/1)	(1/1)	(1/1)	(1/1)	True	True
+freyja			freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja						To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.0	(2/4)	(0/4)	(4/4)	(0/4)	True	True
+frogs			FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis								Up-to-date	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	4.1.0	(0/28)	(0/28)	(0/28)	(28/28)	True	True
+frogs			FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis								Up-to-date	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	4.1.0	(0/28)	(0/28)	(0/28)	(28/28)	True	True
+frogs			FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis								Up-to-date	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	4.1.0	(0/28)	(0/28)	(0/28)	(28/28)	True	True
+frogs			FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom	Suite for metabarcoding analysis								Up-to-date	http://frogs.toulouse.inrae.fr/	Metagenomics	frogs	frogs	https://github.com/geraldinepascal/FROGS-wrappers/	https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs	4.1.0	frogs	4.1.0	(0/28)	(0/28)	(0/28)	(28/28)	True	True
+funannotate			funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate		funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			(3/5)	(5/5)	(5/5)	(5/5)	True	True
+garnett			garnett_check_markers, garnett_classify_cells, garnett_get_feature_genes, garnett_get_std_output, garnett_train_classifier, garnett_transform_markers, update_marker_file	De-composed Garnett functionality tools, see https://github.com/ebi-gene-expression-group/garnett-cli and r-garnett 0.2.8								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_garnett	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/garnett	0.2.8	garnett-cli	0.0.5	(0/7)	(0/7)	(7/7)	(0/7)	True	False
+gblocks			gblocks	Gblocks								Up-to-date	http://molevol.cmima.csic.es/castresana/Gblocks.html	Sequence Analysis	gblocks	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks	0.91b	gblocks	0.91b	(0/1)	(1/1)	(0/1)	(1/1)	True	False
+gdal			gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo	Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats.								To update	https://www.gdal.org	Ecology	gdal	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal	3.0.0			(0/8)	(0/8)	(8/8)	(8/8)	True	False
+gecko	519.0	112.0	gecko	Ungapped genome comparison								Up-to-date	https://github.com/otorreno/gecko	Sequence Analysis	gecko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko	1.2	gecko	1.2	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+gemini	1209.0		gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@	GEMINI: a flexible framework for exploring genome variation	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://github.com/arq5x/gemini	Sequence Analysis, Next Gen Mappers	gemini	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini	0.20.1	gemini	0.30.2	(1/3)	(2/3)	(2/3)	(2/3)	True	False
+geneiobio	44.0	3.0	gene_iobio_display_generation_iframe	Gene.iobio is an interactive tool for variant and trio analysis.								To update	https://github.com/iobio/gene.iobio	Sequence Analysis	geneiobio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio	4.7.1+galaxy1			(0/1)	(1/1)	(1/1)	(0/1)	True	False
+generate_pc_lda_matrix	119.0	12.0	generate_matrix_for_pca_and_lda1	Generate a Matrix for using PC and LDA								To update		Sequence Analysis	generate_pc_lda_matrix	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/generate_pc_lda_matrix	https://github.com/galaxyproject/tools-devteam/tree/main/tools/generate_pc_lda_matrix	1.0.0			(1/1)	(1/1)	(1/1)	(1/1)	True	False
+genomic_super_signature	46.0	11.0	genomic_super_signature	Interpretation of RNAseq experiments through robust, efficient comparison to public databases	genomicsupersignature	genomicsupersignature		GenomicSuperSignature	GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases.	Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction	RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment	To update	https://github.com/shbrief/GenomicSuperSignature	Sequence Analysis, RNA, Transcriptomics	genomic_super_signature	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/genomic_super_signature	https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature	1.2.0	bioconductor-genomicsupersignature	1.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+get_orfs_or_cdss	7.0		get_orfs_or_cdss	Search nucleotide sequences for open reading frames (ORFs), or coding sequences (CDSs)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	Sequence Analysis	get_orfs_or_cdss	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	https://github.com/peterjc/pico_galaxy/tree/master/tools/get_orfs_or_cdss	0.2.3	biopython	1.70	(0/1)	(1/1)	(1/1)	(1/1)	True	False
+getindelrates_3way			indelRates_3way	Estimate Indel Rates for 3-way alignments								To update		Sequence Analysis, Variant Analysis	getindelrates_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindelrates_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindelrates_3way	1.0.0	bx-python	0.11.0	(1/1)	(0/1)	(0/1)	(0/1)	True	False
+getindels_2way			getIndels_2way	Fetch Indels from pairwise alignments								To update		Sequence Analysis, Variant Analysis	getindels_2way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/getindels_2way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/getindels_2way	1.0.0	numpy		(1/1)	(0/1)	(0/1)	(0/1)	True	False
+getmlst			getmlst	Download MLST datasets by species from pubmlst.org								To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+getorganelle	495.0	18.0	get_annotated_regions_from_gb, get_organelle_from_reads	GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data.	getorganelle	getorganelle		GetOrganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data.	De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming	Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms	Up-to-date	https://github.com/Kinggerm/GetOrganelle	Assembly	getorganelle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/getorganelle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle	1.7.7.1	getorganelle	1.7.7.1	(0/2)	(2/2)	(2/2)	(0/2)	True	False
+gfastats	8159.0	418.0	gfastats	Tool for generating sequence statistics and simultaneous genome assembly file manipulation.	gfastats	gfastats		gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.	Data handling	Computational biology	Up-to-date	https://github.com/vgl-hub/gfastats	Sequence Analysis	gfastats	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	https://github.com/bgruening/galaxytools/tree/master/tools/gfastats	1.3.6	gfastats	1.3.6	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+gff3_rebase	110.0	12.0	gff3.rebase	Rebase a GFF against a parent GFF (e.g. an original genome)								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	Sequence Analysis	gff3_rebase	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase	1.2	bcbiogff	0.6.6	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+gffread	10995.0	680.0	gffread	gffread filters and/or converts GFF3/GTF2 records	gffread	gffread		gffread	program for filtering, converting and manipulating GFF files	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/	Sequence Analysis	gffread	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread	0.12.7	gffread	0.12.7	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+ggplot2			ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2		ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		(5/5)	(5/5)	(5/5)	(5/5)	True	True
+gi2taxonomy	660.0	27.0	Fetch Taxonomic Ranks	Fetch taxonomic representation								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+glimmer			glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini		GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	(0/8)	(0/8)	(4/8)	(0/8)	True	True
+glimmer_hmm				GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)								To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm				(0/1)	(0/1)	(0/1)	(0/1)	True	True
+gmaj	11.0	4.0	gmaj_1	GMAJ Multiple Alignment Viewer								To update		Visualization	gmaj	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/gmaj	https://github.com/galaxyproject/tools-devteam/tree/main/tools/gmaj	2.0.1			(1/1)	(1/1)	(1/1)	(1/1)	True	False
+goenrichment	5206.0	321.0	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment		GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de CiĂŞncia.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	(2/2)	(2/2)	(2/2)	(2/2)	True	True
+goseq	19167.0	1210.0	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq		GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+gotohscan	71.0	1.0	rbc_gotohscan	Find subsequences in db								To update		Sequence Analysis	gotohscan	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	https://github.com/bgruening/galaxytools/tree/master/tools/gotohscan	1.3.0	gotohscan	1.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+graphclust	6.0		graphclust	GraphClust can be used for structural clustering of RNA sequences.								To update	http://www.bioinf.uni-freiburg.de/Software/GraphClust/	RNA	graphclust	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	https://github.com/bgruening/galaxytools/tree/master/tools/graphclust	0.1	GraphClust		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+graphlan	5002.0	247.0	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan		GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	(2/2)	(2/2)	(2/2)	(2/2)	True	True
+graphmap			graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap		graphmap	Splice-aware RNA-seq mapper for long reads | GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.3	(0/2)	(0/2)	(2/2)	(0/2)	True	True
+graphprot			graphprot_predict_profile	GraphProt models binding preferences of RNA-binding proteins.								To update	https://github.com/dmaticzka/GraphProt	Sequence Analysis, RNA, CLIP-seq	graphprot	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot	1.1.7+galaxy1	graphprot	1.1.7	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+gsc_high_dimensions_visualisation			high_dimensions_visualisation	Generates PCA, t-SNE and HCPC visualisation								To update	http://artbio.fr	Transcriptomics, Visualization	gsc_high_dimensions_visualisation	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimension_visualization	https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_high_dimensions_visualisation	4.3+galaxy0	r-optparse	1.3.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+gtdbtk			gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 	GTDB-Tk	GTDB-Tk		GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	To update	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.3.2	gtdbtk	2.4.0	(0/1)	(1/1)	(1/1)	(0/1)	True	True
+gtf-2-gene-list			_ensembl_gtf2gene_list	Utility to extract annotations from Ensembl GTF files.								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	gtf2gene_list	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/gtf-2-gene-list	1.52.0+galaxy0	atlas-gene-annotation-manipulation	1.1.1	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+gubbins	3340.0	145.0	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins		Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	(1/1)	(1/1)	(1/1)	(0/1)	True	True
+guppy			guppy-basecaller	A wrapper for the guppy basecaller tool from Oxford Nanopore Technologies								To update	http://artbio.fr	Nanopore	guppy_basecaller	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	https://github.com/ARTbio/tools-artbio/tree/main/tools/guppy	0.2.2			(0/1)	(0/1)	(0/1)	(0/1)	True	False
+gwastools			gwastools_manhattan_plot		gwastools	gwastools		GWASTools	Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.	Deposition, Analysis, Annotation	GWAS study	To update	https://bioconductor.org/packages/release/bioc/html/GWASTools.html	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools	0.1.0	bioconductor-gwastools	1.48.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+hamronization			hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization		hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	(0/2)	(0/2)	(2/2)	(2/2)	True	True
+hansel			bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel		BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+hapcut2			hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	hapcut2	hapcut2		HapCUT2	"HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md"	Haplotype mapping, Variant classification		Up-to-date	https://github.com/vibansal/HapCUT2	Assembly	hapcut2	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2	1.3.4	hapcut2	1.3.4	(0/1)	(1/1)	(0/1)	(0/1)	True	False
+hapog	295.0	36.0	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	hapog	hapog		Hapo-G	Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.	Genome assembly, Optimisation and refinement	Sequence assembly, Genomics	Up-to-date	https://github.com/institut-de-genomique/HAPO-G	Assembly	hapog	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hapog	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog	1.3.8	hapog	1.3.8	(0/1)	(0/1)	(1/1)	(1/1)	True	False
+hardklor	111.0	2.0	hardklor, kronik	Hardklör								To update		Proteomics	hardklor	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/hardklor	2.30.1+galaxy1	hardklor	2.3.2	(0/2)	(0/2)	(2/2)	(0/2)	True	False
+hcluster_sg	238.0	13.0	hcluster_sg	Hierarchically clustering on a sparse graph								To update	https://github.com/douglasgscofield/hcluster	Phylogenetics	hcluster_sg	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg	0.5.1.1	hcluster_sg	0.5.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+hcluster_sg_parser	290.0	7.0	hcluster_sg_parser	Converts hcluster_sg 3-column output into lists of ids								To update	https://github.com/TGAC/earlham-galaxytools/	Phylogenetics	hcluster_sg_parser	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser	0.2.1			(0/1)	(0/1)	(1/1)	(0/1)	True	False
+heatmap2			ggplot2_heatmap2	heatmap.2 function from the R gplots package								To update	https://github.com/cran/gplots	Visualization	ggplot2_heatmap2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heatmap2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2	3.1.3.1	r-gplots	2.17.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+heinz	1186.0	242.0	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	heinz	bionet, heinz		Heinz	Tool for single-species active module discovery.	Pathway or network analysis	Genetics, Gene expression, Molecular interactions, pathways and networks	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz	1.0	bioconductor-bionet	1.62.0	(4/4)	(4/4)	(4/4)	(0/4)	True	False
+helixer	93.0	1.0	helixer	Gene calling with Deep Neural Networks	helixer	helixer		Helixer	Deep Learning to predict gene annotations	Gene prediction, Genome annotation	Sequence analysis, Gene transcripts	To update	https://github.com/weberlab-hhu/Helixer	Genome annotation	helixer	genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	https://github.com/genouest/galaxy-tools/tree/master/tools/helixer	0.3.3			(0/1)	(0/1)	(1/1)	(1/1)	True	False
+hgv_fundo			hgv_funDo	FunDO human genes associated with disease terms								To update		Sequence Analysis	hgv_fundo	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_fundo	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_fundo	1.0.0			(1/1)	(0/1)	(1/1)	(0/1)	True	False
+hgv_hilbertvis			hgv_hilbertvis	HVIS visualization of genomic data with the Hilbert curve								To update	https://www.ebi.ac.uk/huber-srv/hilbert/	Graphics, Visualization	hgv_hilbertvis	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/hgv_hilbertvis	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/hgv/hgv_hilbertvis	1.0.0	R		(1/1)	(0/1)	(1/1)	(0/1)	True	False
+hicexplorer			hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictadclassifier, hicexplorer_hictraintadclassifier, hicexplorer_hictransform, hicexplorer_hicvalidatelocations	HiCExplorer: Set of programs to process, analyze and visualize Hi-C data.								To update	https://github.com/deeptools/HiCExplorer	Sequence Analysis, Visualization	hicexplorer	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer	3.7.2	hicexplorer	3.7.4	(0/40)	(5/40)	(40/40)	(4/40)	True	False
+hicstuff			hicstuff_pipeline									To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff	3.1.5	hicstuff	3.2.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+hifiasm	1410.0	297.0	hifiasm	A fast haplotype-resolved de novo assembler								To update	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	0.19.8	hifiasm	0.19.9	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+hifiasm_meta	137.0	12.0	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta		Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	(0/1)	(1/1)	(1/1)	(0/1)	True	True
+high_dim_heatmap			high_dim_heatmap	gplot heatmap.2 function adapted for plotting large heatmaps								To update	https://github.com/cran/gplots	Visualization	high_dim_heatmap	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/high_dim_heatmap	https://github.com/ARTbio/tools-artbio/tree/main/tools/high_dim_heatmap	3.1.3+galaxy0	r-gplots	2.17.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+hisat	228.0		hisat	HISAT is a fast and sensitive spliced alignment program.								To update	http://ccb.jhu.edu/software/hisat/index.shtml	Assembly	hisat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/hisat	1.0.3	hisat		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+hisat2	299104.0	4183.0	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	hisat2	hisat2		HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).	Sequence alignment	RNA-seq	Up-to-date	http://ccb.jhu.edu/software/hisat2/	Assembly	hisat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2	2.2.1	hisat2	2.2.1	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+hivtrace			hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.								To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+hmmer3	21049.0	111.0	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3		HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	(0/12)	(12/12)	(12/12)	(12/12)	True	True
+homer				Software for motif discovery and next generation sequencing analysis.								To update	http://homer.salk.edu/homer/	Sequence Analysis	homer	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/homer	https://github.com/bgruening/galaxytools/tree/master/tools/homer				(0/1)	(0/1)	(0/1)	(0/1)	True	False
+homer			homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide	HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.	homer	homer		homer	HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein).  It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other.  It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.  HOMER also tries its best to account for sequenced bias in the dataset.  It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem.	Sequence motif discovery		Up-to-date	http://homer.ucsd.edu/homer/index.html	Sequence Analysis	data_manager_homer_preparse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer	4.11	homer	4.11	(0/5)	(0/5)	(5/5)	(4/5)	True	False
+htseq-clip			htseq_clip	htseq-clip is a toolset for the analysis of eCLIP/iCLIP datasets								To update	https://github.com/EMBL-Hentze-group/htseq-clip	Sequence Analysis, RNA, CLIP-seq	htseq_clip	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/htseq-clip	0.1.0+galaxy0	htseq-clip	2.19.0b0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+htseq_count	154533.0	1419.0	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	htseq	htseq		HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data	Nucleic acid sequence analysis	Sequence analysis	Up-to-date	https://readthedocs.org/projects/htseq/	Genomic Interval Operations, SAM, Sequence Analysis, RNA	htseq_count	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count	https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count	2.0.5	htseq	2.0.5	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+humann	5856.0	247.0	humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann		humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	Up-to-date	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.8	humann	3.8	(6/13)	(12/13)	(13/13)	(13/13)	True	True
+hybpiper			hybpiper	Analyse targeted sequence capture data	HybPiper	HybPiper		HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.	Sequence trimming, Sequence assembly, Read mapping	Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics	To update	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper	2.1.6	hybpiper	2.1.7	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+hyphy			hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy		HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.61	(17/17)	(2/17)	(17/17)	(2/17)	True	True
+hypo	354.0	39.0	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo		HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+icescreen			icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen		ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+idba_ud	721.0	43.0	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba		IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	(3/3)	(0/3)	(3/3)	(3/3)	True	True
+idconvert	122.0	3.0	idconvert	Convert mass spectrometry identification files on linux or MacOSX								To update		Proteomics	idconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/idconvert		proteowizard	3_0_9992	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+idr	2873.0	30.0	idr	Galaxy wrappers for the IDR package from Nathan Boleu								To update	https://github.com/nboley/idr	Sequence Analysis	idr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr	2.0.3	idr	2.0.4.2	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+iedb_api	1506.0	12.0	iedb_api	Get epitope binding predictions from IEDB-API								To update	http://tools.immuneepitope.org/main/tools-api/	Data Source, Sequence Analysis	iedb_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api	2.15.2	python		(0/1)	(0/1)	(1/1)	(0/1)	True	False
+illumina_methylation_analyser			illumina_methylation_analyser	Methylation analyzer for Illumina 450k DNA emthylation microarrays								To update	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	Sequence Analysis	illumina_methylation_analyser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	https://github.com/bgruening/galaxytools/tree/master/tools/illumina_methylation_analyser	0.1	Rscript		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+improviser			proteomics_improviser	Visualisation of PepXML files								To update	http://www.improviser.uni-freiburg.de/	Proteomics	proteomics_improviser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	https://github.com/bgruening/galaxytools/tree/master/tools/proteomics/improviser	1.1.0.1			(0/1)	(0/1)	(0/1)	(0/1)	True	False
+indels_3way	22.0		indels_3way	Fetch Indels from 3-way alignments								To update		Sequence Analysis	indels_3way	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/indels_3way	https://github.com/galaxyproject/tools-devteam/tree/main/tools/indels_3way	1.0.3			(1/1)	(0/1)	(1/1)	(0/1)	True	False
+infernal	100230.0	67.0	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities."	infernal	infernal		Infernal	"Infernal (""INFERence of RNA ALignment"") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence."	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	(0/6)	(6/6)	(6/6)	(0/6)	True	True
+inforna				INFO-RNA is a service for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.								To update	http://rna.informatik.uni-freiburg.de/INFORNA/Input.jsp	RNA	inforna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/inforna				(0/1)	(0/1)	(0/1)	(0/1)	True	False
+instagraal	139.0	14.0	instagraal	Large genome reassembly based on Hi-C data	instagraal	instagraal		instaGRAAL	Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL.Large genome reassembly based on Hi-C data, continuation of GRAAL.Large genome reassembly based on Hi-C data (continuation and partial rewrite of GRAAL) and post-scaffolding polishing libraries.This work is under continuous development/improvement - see GRAAL for information about the basic principles.sudo pip3 install -e git+https://github.com/koszullab/instagraal.git@master#egg=instagraal.Note to OS X users: There is currently no CUDA support on Mojave (10.14) and it is unclear when it is going to be added, if it is to be added at all. This means instaGRAAL (or indeed any CUDA-based application) will not work on Mojave. If you wish to run it on OS X, the only solution for now is to downgrade to High Sierra (10.13)	Genome assembly, Mapping assembly, Genetic mapping, Scaffolding	Sequence assembly, Mapping, Metagenomics, Statistics and probability, DNA binding sites	To update	https://github.com/koszullab/instaGRAAL	Assembly	instagraal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	https://github.com/bgruening/galaxytools/tree/master/tools/instagraal	0.1.6			(0/1)	(0/1)	(1/1)	(0/1)	True	False
+instrain			instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain		InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	(0/2)	(0/2)	(2/2)	(0/2)	True	True
+intarna	7569.0	23.0	intarna	Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.								Up-to-date	https://github.com/BackofenLab/IntaRNA	RNA	intarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna	3.4.0	intarna	3.4.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+integron_finder	52965.0	58.0	integron_finder	"""IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"""	integron_finder	integron_finder		Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.3	integron_finder	2.0.3	(0/1)	(1/1)	(1/1)	(1/1)	True	True
+interpolation			interpolation_run_idw_interpolation	Run IDW interpolation based on a .csv and .geojson file								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	1.0	r-getopt		(0/1)	(0/1)	(1/1)	(0/1)	True	False
+interproscan	5294.0	554.0	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi		InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+iprscan5				Interproscan queries the interpro database and provides annotations.								To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5				(0/1)	(0/1)	(0/1)	(0/1)	True	True
+iqtree	21598.0	681.0	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree		iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	To update	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.1.2	iqtree	2.3.3	(1/1)	(1/1)	(1/1)	(0/1)	True	True
+isescan	57581.0	50.0	isescan	"""ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."""	ISEScan	ISEScan		ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	(0/1)	(1/1)	(1/1)	(1/1)	True	True
+isoformswitchanalyzer	822.0	29.0	isoformswitchanalyzer	Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms.	IsoformSwitchAnalyzeR	IsoformSwitchAnalyzeR		IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.	Sequence comparison, Sequence analysis	Computational biology, Gene transcripts	To update	https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html	Transcriptomics, RNA, Statistics	isoformswitchanalyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer	1.20.0	bioconductor-isoformswitchanalyzer	2.2.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+isoplot	2.0	1.0	isoplot	Isoplot is a software for the visualisation of MS data from C13 labelling experiments								To update		Metabolomics, Visualization	isoplot	workflow4metabolomics	https://github.com/llegregam/Isoplot/tree/main	https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot	1.3.0+galaxy1	isoplot	1.3.1	(0/1)	(0/1)	(1/1)	(1/1)	True	False
+itsx	868.0	38.0	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx		ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+ivar			ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing								Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.2	ivar	1.4.2	(5/5)	(5/5)	(5/5)	(5/5)	True	True
+jbrowse	18229.0	2346.0	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse		JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	(2/2)	(2/2)	(2/2)	(2/2)	True	True
+jcvi_gff_stats	2469.0	255.0	jcvi_gff_stats	Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities)								To update	https://github.com/tanghaibao/jcvi	Sequence Analysis	jcvi_gff_stats	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats	0.8.4	jcvi	1.4.11	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+jellyfish	1138.0	91.0	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish		Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	(0/1)	(1/1)	(1/1)	(1/1)	True	True
+kaptive			kaptive	Kaptive reports information about capsular (K) loci found in genome assemblies.								To update		Sequence Analysis	kaptive	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kaptive	0.3.0	kaptive	3.0.0b1	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+kat_filter			kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes								To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+kc-align			kc-align	Kc-Align custom tool	kc-align	kc-align		kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+khmer			khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer		khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	(8/8)	(8/8)	(8/8)	(0/8)	True	True
+kinwalker	70.0	3.0		Kinwalker splits the folding process into a series of events where each event can either be a folding event or a transcription event.								To update	http://www.bioinf.uni-leipzig.de/Software/Kinwalker/	RNA	kinwalker	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker				(0/1)	(0/1)	(0/1)	(0/1)	True	False
+kleborate	319.0	38.0	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate		Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	Up-to-date	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	2.3.2	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+kofamscan	594.0	33.0	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan		kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	(0/1)	(0/1)	(1/1)	(1/1)	True	True
+kraken	13938.0	404.0	kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken	Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm.	kraken	kraken		Kraken	System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken		kraken	1.1.1	(5/5)	(5/5)	(5/5)	(5/5)	True	True
+kraken2	185308.0	2367.0	kraken2	Kraken2 for taxonomic designation.	kraken2	kraken2		kraken2	Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.	Taxonomic classification	Taxonomy, Metagenomics	To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2	2.1.1	kraken2	2.1.3	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+kraken2tax	14683.0	481.0	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk		(1/1)	(1/1)	(1/1)	(0/1)	True	True
+kraken_biom	1444.0	182.0	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)								Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0	(0/1)	(1/1)	(1/1)	(1/1)	True	True
+kraken_taxonomy_report	2527.0	354.0	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report		Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	(1/1)	(1/1)	(1/1)	(0/1)	True	True
+krakentools			krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools		KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	(1/6)	(6/6)	(6/6)	(6/6)	True	True
+krocus			krocus	Predict MLST directly from uncorrected long reads	krocus	krocus		krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+labels			bg_labels	remaps and annotates alignments								To update	https://github.com/bgruening/galaxytools/tree/master/tools/labels	Sequence Analysis	labels	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/labels	https://github.com/bgruening/galaxytools/tree/master/tools/labels	1.0.5.0	labels		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+last	227.0	41.0	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	last	last		LAST	Short read alignment program incorporating quality scores	Sequence alignment	Genomics, Comparative genomics	To update	http://last.cbrc.jp/	Sequence Analysis	last	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/last	https://github.com/galaxyproject/tools-iuc/tree/main/tools/last	1205	last	1542	(0/5)	(0/5)	(5/5)	(5/5)	True	False
+lca_wrapper	137.0	2.0	lca1	Find lowest diagnostic rank								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+legsta	55.0	7.0	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta		legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+length_and_gc_content	4090.0	322.0	length_and_gc_content	Gets gene length and gc content from a fasta and a GTF file								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	Fasta Manipulation, Statistics, RNA, Micro-array Analysis	length_and_gc_content	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content	https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content	0.1.2	r-optparse	1.3.2	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+lfq_protein_quant	111.0	3.0	lfq_protein_quant	Enable protein summarisation and quantitation								To update	https://github.com/compomics/LFQ_galaxy_p	Proteomics	lfq_protein_quant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/lfq_protein_quant	1.0	bioconductor-msnbase	2.28.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+lighter	152.0	9.0	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter		Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+limma_voom	20344.0	1012.0	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma		limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+lineagespot	37.0	2.0	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot		lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		(0/1)	(0/1)	(1/1)	(0/1)	True	True
+links	405.0	77.0	links	Scaffold genome assemblies with long reads.	links	links		LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.	Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming	Sequence assembly, Mapping, Sequencing	Up-to-date	https://github.com/bcgsc/LINKS	Assembly	links	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/links	https://github.com/galaxyproject/tools-iuc/tree/main/tools/links	2.0.1	links	2.0.1	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+locarna			locarna_exparnap, locarna_multiple, locarna_pairwise, locarna_pairwise_p, locarna_reliability_profile	LocARNA - A suite for multiple alignment and folding of RNAs								To update	http://www.bioinf.uni-freiburg.de/Software/LocARNA/	RNA	locarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna	1.9.2.3	locarna	2.0.0	(0/5)	(0/5)	(1/5)	(0/5)	True	False
+logistic_regression_vif			LogisticRegression	Perform Logistic Regression with vif								To update		Sequence Analysis, Variant Analysis, Statistics	logistic_regression_vif	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/logistic_regression_vif	https://github.com/galaxyproject/tools-devteam/tree/main/tools/logistic_regression_vif	1.0.1	numpy		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+logol			logol_wrapper	Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence								Up-to-date	http://logol.genouest.org/web/app.php/logol	Sequence Analysis		genouest	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	https://github.com/genouest/galaxy-tools/tree/master/tools/logol	1.7.8	logol	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+lorikeet			lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet		lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+lotus2	936.0	114.0	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2		lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	Up-to-date	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.32	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+m6anet	3.0		m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet		m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+maaslin2	188.0	29.0	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2		MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	To update	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	0.99.12	maaslin2	1.16.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+macs2	84202.0	1968.0	macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak	MACS - Model-based Analysis of ChIP-Seq	macs	macs		MACS	Model-based Analysis of ChIP-seq data.	Peak calling, Enrichment analysis, Gene regulatory network analysis	ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites	Up-to-date	https://github.com/taoliu/MACS	Sequence Analysis, Statistics	macs2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2	2.2.9.1	macs2	2.2.9.1	(9/9)	(9/9)	(9/9)	(9/9)	True	False
+maf_cpg_filter			cpgFilter	Mask CpG/non-CpG sites from MAF file								To update		Sequence Analysis, Variant Analysis	maf_cpg_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/maf_cpg_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/maf_cpg_filter	1.0.0	bx-python	0.11.0	(1/1)	(0/1)	(0/1)	(0/1)	True	False
+mafft	143045.0	817.0	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT		MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.520	mafft	7.525	(2/2)	(2/2)	(2/2)	(2/2)	True	True
+make_nr			make_nr	Make a FASTA file non-redundant								To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	Fasta Manipulation, Sequence Analysis	make_nr	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr	0.0.2	biopython	1.70	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+maker	4950.0	419.0	maker, maker_map_ids	MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	maker	maker		MAKER	Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.	Genome annotation	Genomics, DNA, Sequence analysis	To update	http://www.yandell-lab.org/software/maker.html	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker	2.31.11	maker	3.01.03	(2/2)	(2/2)	(2/2)	(2/2)	True	True
+maldiquant			maldi_quant_peak_detection, maldi_quant_preprocessing	MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data.								To update	http://strimmerlab.org/software/maldiquant/	Proteomics	MALDIquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maldiquant	1.22.0	r-base		(0/2)	(2/2)	(2/2)	(2/2)	True	False
+map_peptides_to_bed	41.0	1.0	map_peptides_to_bed	Map peptides to a reference genome for display by a genome browser								To update		Proteomics	map_peptides_to_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/map_peptides_to_bed	0.2	biopython	1.70	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+mapping_quality_stats			mapqstatistics	Collects and shows the distribution of MAPQ values in a BAM alignment file								To update	http://artbio.fr	Sequence Analysis, Statistics	mapping_quality_stats	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats	0.22.0	r-optparse	1.3.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+mapping_to_ucsc			mapToUCSC	Format mapping data as UCSC custom track								To update		Visualization, Convert Formats, Next Gen Mappers	mapping_to_ucsc	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/mapping_to_ucsc	https://github.com/galaxyproject/tools-devteam/tree/main/tools/mapping_to_ucsc	1.0.0			(0/1)	(0/1)	(0/1)	(0/1)	True	False
+mapseq	167.0	2.0	mapseq	fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.	mapseq	mapseq		MAPseq	Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis .	k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	To update	https://github.com/jfmrod/MAPseq	Metagenomics	mapseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq	2.1.1	perl		(0/1)	(0/1)	(1/1)	(0/1)	True	True
+mash	1739.0	12.0	mash_screen, mash_sketch	Fast genome and metagenome distance estimation using MinHash	mash	mash		Mash	Fast genome and metagenome distance estimation using MinHash.	Sequence distance matrix generation	Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	Up-to-date	https://github.com/marbl/Mash	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash	2.3	mash	2.3	(2/2)	(2/2)	(2/2)	(2/2)	True	True
+mashmap			mashmap	Fast local alignment boundaries								Up-to-date	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	Sequence Analysis	mashmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap	3.1.3	mashmap	3.1.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+masigpro	576.0	13.0	masigpro	Identify significantly differential expression profiles in time-course microarray experiments	masigpro	masigpro		maSigPro	Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.	Regression analysis	Gene expression, Molecular genetics, Microarray experiment, RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html	Transcriptomics, RNA, Statistics	masigpro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro	https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro	1.49.3	coreutils	8.25	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+mauve_contig_mover			mauve_contig_mover	Order a draft genome relative to a related reference genome								To update	https://github.com/phac-nml/mauve_contig_mover	Sequence Analysis	mauve_contig_mover	nml	https://github.com/phac-nml/mauve_contig_mover	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mauve_contig_mover	1.0.10	mauve	2.4.0.r4736	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+maxbin2	2059.0	118.0	maxbin2	clusters metagenomic contigs into bins	maxbin	maxbin		MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	To update	https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html	Metagenomics	maxbin2	mbernt	https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2		maxbin2	2.2.7	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+maxquant	5804.0	407.0	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant		MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	(2/2)	(2/2)	(2/2)	(0/2)	True	True
+mcl	29.0	10.0	mcl	The Markov Cluster Algorithm, a cluster algorithm for graphs	mcl	mcl		MCL	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.	Clustering, Network analysis, Gene regulatory network analysis	Molecular interactions, pathways and networks	Up-to-date	https://micans.org/mcl/man/mcl.html	Sequence Analysis	mcl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/mcl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl	22.282	mcl	22.282	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+mea	85.0	3.0	mea	Maximum expected accuracy prediction								To update	http://www.bioinf.uni-leipzig.de/Software/mea	RNA	mea	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mea	0.6.4.1	mea	0.6.4	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+mean-per-zone			mean_per_zone	Creates a png image showing statistic over areas as defined in the vector file								To update	https://github.com/NordicESMhub/galaxy-tools/blob/master/tools/mean-per-zone/	Visualization, GIS, Climate Analysis	mean_per_zone	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone	0.2.0	python		(0/1)	(0/1)	(1/1)	(0/1)	True	False
+medaka			medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka		Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	1.11.3	(3/4)	(3/4)	(3/4)	(3/4)	True	True
+medenv			iabiodiv_smartbiodiv_med_environ	Retrieve environmental data from etopo, cmems and woa								To update	https://github.com/jeremyfix/medenv	Ecology, Data Source		ecology	https://github.com/jeremyfix/medenv	https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv	0.1.0	pandas		(0/1)	(0/1)	(1/1)	(0/1)	True	False
+megahit	9530.0	548.0	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+megahit_contig2fastg	475.0	54.0	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit		MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+megan			megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data.  MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan		MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzerÂť) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	(0/7)	(0/7)	(7/7)	(0/7)	True	True
+meningotype			meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype		meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+merqury	2483.0	244.0	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury		Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	(2/2)	(2/2)	(2/2)	(2/2)	True	True
+meryl	6785.0	350.0	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl		Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	(0/7)	(0/7)	(0/7)	(0/7)	True	True
+meta_proteome_analyzer	123.0	10.0	meta_proteome_analyzer	MetaProteomeAnalyzer								Up-to-date	https://github.com/compomics/meta-proteome-analyzer/	Proteomics	meta_proteome_analyzer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/meta_proteome_analyzer	2.0.0	mpa-portable	2.0.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+metabat2	4072.0	154.0	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2		MetaBAT 2	"an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning"	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	Up-to-date	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.15	(2/2)	(1/2)	(2/2)	(2/2)	True	True
+metaeuk			metaeuk_easy_predict	MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 	MetaEuk	MetaEuk		MetaEuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics	Homology-based gene prediction	Metagenomics, Gene and protein families	To update	https://github.com/soedinglab/metaeuk	Sequence Analysis, Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk	5.34c21f2	metaeuk	6.a5d39d9	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+metagene_annotator	636.0	115.0	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator		MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+metagenomeseq			metagenomeseq_normalizaton	metagenomeSeq Normalization	metagenomeseq	metagenomeseq		metagenomeSeq	Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	To update		Metagenomics	metagenomeseq_normalization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq	1.16.0-0.0.1	bioconductor-metagenomeseq	1.43.0	(1/1)	(0/1)	(1/1)	(1/1)	True	True
+metanovo	4181.0	15.0	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo		MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+metaphlan	10507.0	427.0	customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan	MetaPhlAn for Metagenomic Phylogenetic Analysis	metaphlan	metaphlan		MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.	Nucleic acid sequence analysis, Phylogenetic tree analysis	Metagenomics, Phylogenomics	To update	https://github.com/biobakery/MetaPhlAn	Metagenomics	metaphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan	4.0.6	metaphlan	4.1.0	(1/4)	(2/4)	(4/4)	(4/4)	True	True
+metaquantome			metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome		metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	(0/6)	(6/6)	(6/6)	(0/6)	True	True
+metawrapmg			metawrapmg_binning	A flexible pipeline for genome-resolved metagenomic data analysis	metawrap	metawrap		MetaWRAP	MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation.	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	Up-to-date	https://github.com/bxlab/metaWRAP	Metagenomics	metawrapmg_binning	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg	1.3.0	metawrap-mg	1.3.0	(0/1)	(1/1)	(1/1)	(0/1)	True	True
+methtools			methtools_calling, r_correlation_matrix, methtools_destrand, methtools_dmr, methtools_filter, methtools_plot, smooth_running_window, methtools_tiling	tools for methylation analysis								To update	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	Sequence Analysis	methtools	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	https://github.com/bgruening/galaxytools/tree/master/tools/methtools	0.1.1	methtools		(0/8)	(0/8)	(0/8)	(0/8)	True	False
+methyldackel			pileometh	A tool for processing bisulfite sequencing alignments								To update	https://github.com/dpryan79/MethylDackel	Sequence Analysis	pileometh	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel	0.5.2	methyldackel	0.6.1	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+metilene	3966.0	103.0	metilene	Differential DNA methylation calling								To update		RNA, Statistics	metilene	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	https://github.com/bgruening/galaxytools/tree/master/tools/metilene	0.2.6.1	metilene	0.2.8	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+miclip			mi_clip	Identification of binding sites in CLIP-Seq data.								To update	https://cran.r-project.org/src/contrib/Archive/MiClip/	Sequence Analysis	miclip	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	https://github.com/bgruening/galaxytools/tree/master/tools/miclip	1.2.0	Rscript		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+microsatellite_birthdeath			microsatellite_birthdeath	Identify microsatellite births and deaths								To update		Sequence Analysis	microsatellite_birthdeath	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsatellite_birthdeath	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsatellite_birthdeath	1.0.0			(0/1)	(0/1)	(0/1)	(0/1)	True	False
+microsats_alignment_level			microsats_align1	Extract Orthologous Microsatellites from pair-wise alignments								To update		Sequence Analysis, Variant Analysis	microsats_alignment_level	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_alignment_level	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_alignment_level	1.0.0	sputnik		(1/1)	(0/1)	(0/1)	(0/1)	True	False
+microsats_mutability			microsats_mutability1	Estimate microsatellite mutability by specified attributes								To update		Sequence Analysis, Variant Analysis	microsats_mutability	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/microsats_mutability	https://github.com/galaxyproject/tools-devteam/tree/main/tools/microsats_mutability	1.1.0	bx-python	0.11.0	(1/1)	(0/1)	(0/1)	(0/1)	True	False
+migmap	1226.0	7.0	migmap	mapper for full-length T- and B-cell repertoire sequencing	MiGMAP	MiGMAP		MiGMAP	Mapper for full-length T- and B-cell repertoire sequencing.	Sequence analysis, Read mapping	Immunoproteins, genes and antigens, Sequence analysis	Up-to-date	https://github.com/mikessh/migmap	RNA, Sequence Analysis	migmap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap	1.0.3	migmap	1.0.3	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+minced	895.0	53.0	minced	MinCED - Mining CRISPRs in Environmental Datasets								To update	http://bioweb2.pasteur.fr/docs/modules/minced/0.1.5/_README	Sequence Analysis	minced	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minced	https://github.com/bgruening/galaxytools/tree/master/tools/minced	0.2.0	minced	0.4.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+minia	2206.0	109.0	minia	Short-read assembler based on a de Bruijn graph	minia	minia		Minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.	Genome assembly	Sequence assembly	Up-to-date	https://gatb.inria.fr/software/minia/	Assembly	minia	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia	https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia	3.2.6	minia	3.2.6	(0/1)	(1/1)	(1/1)	(0/1)	True	True
+miniasm	11938.0	178.0	miniasm	Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step)	miniasm	miniasm		miniasm	Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format.	De-novo assembly	Genomics, Sequence assembly	To update	https://github.com/lh3/miniasm	Assembly	miniasm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm	0.3_r179	miniasm	0.3	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+minipolish	185.0	21.0	minipolish	Polishing miniasm assemblies	minipolish	minipolish		minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+miniprot	813.0	15.0	miniprot, miniprot_index	Align a protein sequence against a genome with affine gap penalty, splicing and frameshift.	miniprot	miniprot		miniprot	Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	Up-to-date	https://github.com/lh3/miniprot	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot	0.13	miniprot	0.13	(0/2)	(0/2)	(2/2)	(2/2)	True	True
+miranda	6076.0	41.0	miranda	Finds potential target sites for miRNAs in genomic sequences								To update	http://www.microrna.org/	RNA	miranda	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/miranda	3.3a+galaxy1	miranda	3.3a	(0/1)	(0/1)	(1/1)	(1/1)	True	False
+mircounts			mircounts	Generates miRNA count lists from read alignments to mirBase.								To update	http://artbio.fr	RNA, Transcriptomics	mircounts	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts	https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts	1.6	tar		(0/1)	(1/1)	(0/1)	(0/1)	True	False
+mirmachine			mirmachine	Tool to detect miRNA in genome sequences								Up-to-date	https://github.com/sinanugur/MirMachine	Sequence Analysis	mirmachine	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine	0.2.13	mirmachine	0.2.13	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+mirnature	10.0	4.0	mirnature	Computational detection of canonical microRNAs								Up-to-date	https://github.com/Bierinformatik/miRNAture	RNA, Sequence Analysis	mirnature	iuc	https://github.com/Bierinformatik/miRNAture	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature	1.1	mirnature	1.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+mitobim	881.0	66.0	mitobim	assemble mitochondrial genomes								Up-to-date	https://github.com/chrishah/MITObim	Assembly	mitobim	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim	1.9.1	mitobim	1.9.1	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+mitohifi	613.0	56.0	mitohifi	Assembly mitogenomes from Pacbio HiFi read.								To update	https://github.com/marcelauliano/MitoHiFi/tree/mitohifi_v2	Assembly	mitohifi	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi	3			(1/1)	(1/1)	(1/1)	(0/1)	True	False
+mitos	32022.0	58.0	mitos, mitos2	de-novo annotation of metazoan mitochondrial genomes	mitos	mitos		MITOS	De novo metazoan mitochondrial genome annotation.	Genome annotation	Zoology, Whole genome sequencing	To update	http://mitos.bioinf.uni-leipzig.de/	Sequence Analysis	mitos	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos	1.1.7	mitos	2.1.9	(1/2)	(1/2)	(2/2)	(0/2)	True	True
+mlst	9304.0	635.0	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst		MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	(2/2)	(2/2)	(2/2)	(2/2)	True	True
+moFF			proteomics_moff	moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files.								Up-to-date	https://github.com/compomics/moFF	Proteomics	proteomics_moff	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF	2.0.3	moff	2.0.3	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+mob_suite	89021.0	322.0	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies								To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.8	(0/2)	(2/2)	(2/2)	(2/2)	True	True
+monocle3			monocle3_create, monocle3_diffExp, monocle3_learnGraph, monocle3_orderCells, monocle3_partition, monocle3_plotCells, monocle3_preprocess, monocle3_reduceDim, monocle3_topmarkers	De-composed monocle3 functionality tools, based on https://github.com/ebi-gene-expression-group/monocle-scripts and monocle3 0.1.2.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_monocle3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/monocle3	0.1.4	monocle3-cli	0.0.9	(9/9)	(0/9)	(9/9)	(0/9)	True	False
+morpheus	140.0	4.0	morpheus	Morpheus MS Search Application								To update		Proteomics	morpheus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/morpheus	2.255.0	morpheus	288	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+mothur			mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur		mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	(129/129)	(129/129)	(129/129)	(129/129)	True	True
+mqc	76.0	5.0	mqc	Ribosome profiling mapping quality control tool								To update	https://github.com/Biobix/mQC	Sequence Analysis	mqc	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/mqc	1.9	mqc	1.10	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+mqppep			mqppep_anova, mqppep_preproc	MaxQuant Phosphoproteomic Enrichment Pipeline - Preprocessing and ANOVA								To update	https://github.com/galaxyproteomics/tools-galaxyp/	Proteomics	mqppep	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep	0.1.19	bioconductor-preprocesscore	1.64.0	(0/2)	(0/2)	(2/2)	(0/2)	True	False
+mrbayes			mrbayes	A program for the Bayesian estimation of phylogeny.								To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+msconvert	20406.0	190.0	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert		msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			(1/1)	(1/1)	(1/1)	(1/1)	True	True
+msgfplus	507.0	5.0	msgfplus	MSGF+								To update		Proteomics	msgfplus	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msgfplus	0.5	msgf_plus	2024.03.26	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+msms_extractor	110.0	1.0	msms_extractor	Extract MS/MS scans from the mzML file(s) based on PSM report.								To update		Proteomics	msms_extractor	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msms_extractor	1.0.0	proteowizard	3_0_9992	(0/1)	(0/1)	(1/1)	(1/1)	True	False
+msstats	2036.0	144.0	msstats	MSstats tool for analyzing mass spectrometry proteomic datasets	msstatstmt	msstatstmt		MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling	Spectrum calculation, Tag-based peptide identification, Differential protein expression profiling	Proteomics, Proteomics experiment, Protein expression	To update	https://github.com/MeenaChoi/MSstats	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstats	4.0.0	bioconductor-msstats	4.10.0	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+msstatstmt	726.0	71.0	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling								To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0	(0/1)	(1/1)	(1/1)	(0/1)	True	True
+mt2mq	270.0	19.0	mt2mq	Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome								To update		Proteomics	mt2mq	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mt2mq	1.1.0	r-tidyverse		(0/1)	(0/1)	(1/1)	(0/1)	True	False
+multigsea	53.0	2.0	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA		multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+multiqc	162790.0	8320.0	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc		MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.11	multiqc	1.21	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+multispecies_orthologous_microsats			multispecies_orthologous_microsats	Extract orthologous microsatellites								To update		Sequence Analysis, Variant Analysis	multispecies_orthologous_microsats	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/multispecies_orthologous_microsats	https://github.com/galaxyproject/tools-devteam/tree/main/tools/multispecies_orthologous_microsats	1.0.0	bx-sputnik		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+mummer	652.0	83.0	mummerplot_wrapper	Draw dotplots using mummer, mucmer, or promer with mummerplot								To update	http://mummer.sourceforge.net/	Graphics, Sequence Analysis, Visualization	mummer	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	https://github.com/peterjc/pico_galaxy/tree/master/tools/mummer	0.0.8	ghostscript	9.18	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+mummer4			mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords	Mummer4 Tools	mummer4	mummer4						Up-to-date	https://github.com/mummer4/mummer	Sequence Analysis	mummer4	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4	4.0.0rc1	mummer4	4.0.0rc1	(6/6)	(6/6)	(6/6)	(6/6)	True	False
+mykrobe			mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe		Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+mykrobe_parser			mykrobe_parseR	RScript to parse the results of mykrobe predictor.								To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base		(0/1)	(0/1)	(0/1)	(0/1)	True	True
+mz_to_sqlite	844.0	33.0	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite		mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	(1/1)	(1/1)	(1/1)	(0/1)	True	True
+mzml_validator			mzml_validator	mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.								To update	https://github.com/RECETOX/galaxytools	Metabolomics, Proteomics		recetox	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	https://github.com/RECETOX/galaxytools/tree/master/tools/mzml_validator	0.1.0+galaxy2	lxml		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+naltorfs			bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs	nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs)								Up-to-date	https://github.com/BlankenbergLab/nAltORFs	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs	0.1.2	naltorfs	0.1.2	(3/3)	(0/3)	(0/3)	(0/3)	True	False
+nanocompore			nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore		Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	(0/2)	(1/2)	(2/2)	(0/2)	True	True
+nanoplot	63235.0	2195.0	nanoplot	Plotting tool for long read sequencing data and alignments	nanoplot	nanoplot		NanoPlot	NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences	Scatter plot plotting, Box-Whisker plot plotting	Genomics	Up-to-date	https://github.com/wdecoster/NanoPlot	Visualization	nanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot	1.42.0	nanoplot	1.42.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+nanopolishcomp			nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate	NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation.	nanopolishcomp	nanopolishcomp		NanopolishComp	NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish.	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	To update	https://a-slide.github.io/NanopolishComp	Sequence Analysis	nanopolishcomp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp	0.6.11	nanopolishcomp	0.6.12	(0/2)	(0/2)	(2/2)	(2/2)	True	True
+nastiseq	40.0		nastiseq	A method to identify cis-NATs using ssRNA-seq								Up-to-date	https://ohlerlab.mdc-berlin.de/software/NASTIseq_104/	RNA	nastiseq	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/nastiseq	1.0	r-nastiseq	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+ncbi_blast_plus	365597.0	4066.0	blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper	NCBI BLAST+								To update	https://blast.ncbi.nlm.nih.gov/	Sequence Analysis	ncbi_blast_plus	devteam	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus	2.14.1	python		(16/18)	(16/18)	(16/18)	(16/18)	True	True
+ncbi_fcs_adaptor			ncbi_fcs_adaptor	FCS-adaptor detects adaptor and vector contamination in genome sequences.								To update	https://github.com/ncbi/fcs	Sequence Analysis	ncbi_fcs_adaptor	richard-burhans	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor	0.5.0			(1/1)	(0/1)	(0/1)	(0/1)	True	False
+ncbi_fcs_gx			ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).								Up-to-date	https://github.com/ncbi/fcs-gx	Sequence Analysis	ncbi_fcs_gx	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx	0.5.0	ncbi-fcs-gx	0.5.0	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+necat	667.0	95.0	necat	Error correction and de-novo assembly for ONT Nanopore reads	necat	necat		NECAT	NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads.	De-novo assembly	Sequence assembly	Up-to-date	https://github.com/xiaochuanle/NECAT	Assembly	necat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat	0.0.1_update20200803	necat	0.0.1_update20200803	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+newick_utils	25505.0	448.0	newick_display	Perform operations on Newick trees	newick_utilities	newick_utilities		Newick Utilities	The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.	Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction	Phylogeny, Genomics, Computer science	To update	http://cegg.unige.ch/newick_utils	Visualization, Metagenomics	newick_utils	iuc	https://github.com/tjunier/newick_utils	https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils	1.6+galaxy1	newick_utils	1.6	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+nextclade	3527.0	169.0	nextalign, nextclade	Identify differences between your sequences and a reference sequence used by Nextstrain	nextclade	nextclade		Nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.	Methylation analysis, Variant calling	Genomics, Sequence analysis, Cladistics	To update	https://github.com/nextstrain/nextclade	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade	2.7.0	nextalign	2.14.0	(1/2)	(1/2)	(2/2)	(2/2)	True	True
+nextdenovo	268.0	84.0	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo		NextDenovo	"NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a ""correct-then-assemble"" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages."	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+nlstradamus			nlstradamus	Find nuclear localization signals (NLSs) in protein sequences								To update	http://www.moseslab.csb.utoronto.ca/NLStradamus	Fasta Manipulation, Sequence Analysis	nlstradamus	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	https://github.com/peterjc/pico_galaxy/tree/master/tools/nlstradamus	0.0.11	NLStradamus	1.8	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+nonpareil	142.0	5.0	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil		nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.4.1	(1/1)	(0/1)	(1/1)	(1/1)	True	True
+novoplasty	6384.0	162.0	novoplasty	NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes.								To update	https://github.com/ndierckx/NOVOPlasty	Assembly	novoplasty	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty	https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty	4.3.1	novoplasty	4.3.5	(0/1)	(1/1)	(1/1)	(1/1)	True	False
+nucleosome_prediction	861.0	2.0	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction		nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+nugen_nudup			nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.	nudup	nudup		NuDup	Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products.	Duplication detection	Sequencing	Up-to-date	https://github.com/tecangenomics/nudup	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup	2.3.3	nudup	2.3.3	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+oases			oasesoptimiserv	Short read assembler								To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	https://github.com/ARTbio/tools-artbio/tree/main/tools/oases	1.4.0	oases	0.2.09	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+obisindicators	45.0	4.0	obisindicators, obis_data	Compute biodiveristy indicators for marine data from obis								To update	https://github.com/Marie59/obisindicators	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators	0.0.2	r-base		(1/2)	(0/2)	(2/2)	(1/2)	True	True
+obitools			obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq	OBITools is a set of programs developed to simplify the manipulation of sequence files	obitools	obitools		OBITools	Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding.	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	Up-to-date	http://metabarcoding.org/obitools	Sequence Analysis	obitools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools	1.2.13	obitools	1.2.13	(0/10)	(10/10)	(10/10)	(10/10)	True	True
+ocean			argo_getdata	Access, process, visualise oceanographic data for the Earth System								To update	https://github.com/Marie59/FE-ft-ESG/tree/main/argo	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean	0.1.15			(0/1)	(0/1)	(1/1)	(0/1)	True	False
+odgi			odgi_build, odgi_viz	Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it.								To update	https://github.com/vgteam/odgi	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi	0.3	odgi	0.8.6	(0/2)	(0/2)	(2/2)	(2/2)	True	False
+ogcProcess_otb_bandmath			otb_band_math	Outputs a monoband image which is the result of a mathematical operation on several multi-band images.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath	1.0	r-base		(0/1)	(0/1)	(1/1)	(0/1)	True	False
+ogcProcess_otb_meanShiftSmoothing			otb_mean_shift_smoothing	This application smooths an image using the MeanShift algorithm.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing	1.0	r-base		(0/1)	(0/1)	(1/1)	(0/1)	True	False
+omark			omark	Proteome quality assessment software	omark	omark		OMArk	Proteome quality assessment software	Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	To update	https://github.com/DessimozLab/OMArk	Sequence Analysis	omark	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark	0.3.0			(0/1)	(0/1)	(1/1)	(1/1)	True	True
+ont_fast5_api			ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5	ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.								To update	https://github.com/nanoporetech/ont_fast5_api/	Nanopore	ont_fast5_api	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api	3.1.3	ont-fast5-api	4.1.3	(0/4)	(0/4)	(4/4)	(0/4)	True	False
+openms			AccurateMassSearch, AssayGeneratorMetabo, BaselineFilter, CVInspector, ClusterMassTraces, ClusterMassTracesByPrecursor, CometAdapter, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, CruxAdapter, DTAExtractor, DatabaseFilter, DatabaseSuitability, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, Epifany, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledKD, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, GNPSExport, HighResPrecursorMassCorrector, IDConflictResolver, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSFraggerAdapter, MSGFPlusAdapter, MSSimulator, MSstatsConverter, MaRaClusterAdapter, MapAlignerIdentification, MapAlignerPoseClustering, MapAlignerSpectrum, MapAlignerTreeGuided, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteAdductDecharger, MetaboliteSpectralMatcher, MultiplexResolver, MyriMatchAdapter, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, NovorAdapter, NucleicAcidSearchEngine, OMSSAAdapter, OpenMSDatabasesInfo, OpenPepXL, OpenPepXLLF, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PSMFeatureExtractor, PTModel, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PercolatorAdapter, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, QualityControl, RNADigestor, RNAMassCalculator, RNPxlSearch, RNPxlXICFilter, RTEvaluation, RTModel, SeedListGenerator, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SiriusAdapter, SpecLibCreator, SpecLibSearcher, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SpectraSTSearchAdapter, StaticModification, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TOFCalibration, TargetedFileConverter, TextExporter, TransformationEvaluation, TriqlerConverter, XFDR, XMLValidator, XTandemAdapter	OpenMS Suite for LC/MS data management and analyses								To update	https://www.openms.de/	Proteomics	openms	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms	2.8	openms	3.1.0	(8/164)	(35/164)	(160/164)	(0/164)	True	False
+openms			AccurateMassSearch, AdditiveSeries, BaselineFilter, CVInspector, CompNovo, CompNovoCID, ConsensusID, ConsensusMapNormalizer, ConvertTSVToTraML, ConvertTraMLToTSV, DTAExtractor, DeMeanderize, Decharger, DecoyDatabase, Digestor, DigestorMotif, EICExtractor, ERPairFinder, ExternalCalibration, FFEval, FalseDiscoveryRate, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderIsotopeWavelet, FeatureFinderMRM, FeatureFinderMetabo, FeatureFinderMultiplex, FeatureFinderSuperHirn, FeatureLinkerLabeled, FeatureLinkerUnlabeled, FeatureLinkerUnlabeledQT, FidoAdapter, FileConverter, FileFilter, FileInfo, FileMerger, FuzzyDiff, HighResPrecursorMassCorrector, IDConflictResolver, IDDecoyProbability, IDExtractor, IDFileConverter, IDFilter, IDMapper, IDMassAccuracy, IDMerger, IDPosteriorErrorProbability, IDRTCalibration, IDRipper, IDScoreSwitcher, IDSplitter, ITRAQAnalyzer, InclusionExclusionListCreator, InspectAdapter, InternalCalibration, IsobaricAnalyzer, LabeledEval, LowMemPeakPickerHiRes, LowMemPeakPickerHiRes_RandomAccess, LuciphorAdapter, MRMMapper, MRMPairFinder, MRMTransitionGroupPicker, MSGFPlusAdapter, MSSimulator, MapAlignmentEvaluation, MapNormalizer, MapRTTransformer, MapStatistics, MascotAdapter, MascotAdapterOnline, MassCalculator, MassTraceExtractor, MetaProSIP, MetaboliteSpectralMatcher, MultiplexResolver, MzMLSplitter, MzTabExporter, NoiseFilterGaussian, NoiseFilterSGolay, OpenSwathAnalyzer, OpenSwathAssayGenerator, OpenSwathChromatogramExtractor, OpenSwathConfidenceScoring, OpenSwathDIAPreScoring, OpenSwathDecoyGenerator, OpenSwathFeatureXMLToTSV, OpenSwathFileSplitter, OpenSwathMzMLFileCacher, OpenSwathRTNormalizer, OpenSwathRewriteToFeatureXML, OpenSwathWorkflow, PTModel, PTPredict, PeakPickerHiRes, PeakPickerIterative, PeakPickerWavelet, PepNovoAdapter, PeptideIndexer, PhosphoScoring, PrecursorIonSelector, PrecursorMassCorrector, ProteinInference, ProteinQuantifier, ProteinResolver, QCCalculator, QCEmbedder, QCExporter, QCExtractor, QCImporter, QCMerger, QCShrinker, RNPxl, RNPxlXICFilter, RTEvaluation, RTModel, RTPredict, SemanticValidator, SequenceCoverageCalculator, SimpleSearchEngine, SpecLibCreator, SpectraFilterBernNorm, SpectraFilterMarkerMower, SpectraFilterNLargest, SpectraFilterNormalizer, SpectraFilterParentPeakMower, SpectraFilterScaler, SpectraFilterSqrtMower, SpectraFilterThresholdMower, SpectraFilterWindowMower, SpectraMerger, SvmTheoreticalSpectrumGeneratorTrainer, TICCalculator, TMTAnalyzer, TOFCalibration, TextExporter, TopPerc, TransformationEvaluation, XMLValidator, XTandemAdapter	OpenMS in version 2.1.								To update		Proteomics	openms	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/openms	https://github.com/bgruening/galaxytools/tree/master/tools/openms	2.1.0	openms	3.1.0	(7/140)	(34/140)	(135/140)	(0/140)	True	False
+optitype	321.0	24.0	optitype	Precision HLA typing from NGS data								Up-to-date	https://github.com/FRED-2/OptiType	Sequence Analysis	optitype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1	https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype	1.3.5	optitype	1.3.5	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+orfipy	774.0	53.0	orfipy	Galaxy wrapper for ORFIPY	orfipy	orfipy		orfipy	A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here.	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	Up-to-date	https://github.com/urmi-21/orfipy	Sequence Analysis	orfipy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy	0.0.4	orfipy	0.0.4	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+orthofinder			orthofinder_onlygroups	Accurate inference of orthologous gene groups made easy	OrthoFinder	OrthoFinder		OrthoFinder	OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses.	Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis	Up-to-date	https://github.com/davidemms/OrthoFinder	Phylogenetics, Sequence Analysis	orthofinder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder	2.5.5	orthofinder	2.5.5	(0/1)	(1/1)	(1/1)	(1/1)	True	True
+pairtools			pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats	Flexible tools for Hi-C data processing								Up-to-date	https://pairtools.readthedocs.io	Sequence Analysis	pairtools	iuc	https://github.com/open2c/pairtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools	1.1.0	pairtools	1.1.0	(5/5)	(0/5)	(5/5)	(0/5)	True	False
+pangolin	7276.0	259.0	pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages								To update	https://github.com/hCoV-2019/pangolin	Sequence Analysis	pangolin	nml	https://github.com/hCoV-2019/pangolin	https://github.com/phac-nml/galaxy_tools/tree/master/tools/pangolin	1.1.14	pangolin	4.3	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+pangolin	7276.0	259.0	pangolin	Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system.	pangolin_cov-lineages	pangolin_cov-lineages		pangolin	Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages	Tree-based sequence alignment, Variant classification	Virology	Up-to-date	https://github.com/cov-lineages/pangolin	Sequence Analysis	pangolin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin	4.3	pangolin	4.3	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+paralyzer	299.0	7.0	paralyzer	A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets.								Up-to-date	https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/	RNA	paralyzer	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer	1.5	paralyzer	1.5	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+parse_mito_blast	90.0	31.0	parse_mito_blast	Filtering blast out from querying assembly against mitochondrial database.								Up-to-date	https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py	Sequence Analysis	parse_mito_blast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast	1.0.2	parse_mito_blast	1.0.2	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+pathview	5260.0	565.0	pathview	Pathview is a tool set for pathway based data integration and visualization.	pathview	pathview		pathview	Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.	Pathway or network analysis, Pathway or network visualisation	Molecular interactions, pathways and networks, Systems biology, Data visualisation	To update	https://bioconductor.org/packages/release/bioc/html/pathview.html	Statistics, RNA, Micro-array Analysis	pathview	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview	1.34.0	bioconductor-pathview	1.42.0	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+pathwaymatcher			reactome_pathwaymatcher	Reactome Pathway Matcher								To update	https://github.com/LuisFranciscoHS/PathwayMatcher	Proteomics	reactome_pathwaymatcher	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pathwaymatcher		pathwaymatcher	1.9.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+patrist			patrist	Extract Patristic Distance From a Tree								To update	https://gist.github.com/ArtPoon/7330231e74201ded54b87142a1d6cd02	Phylogenetics	patrist	nml	https://github.com/phac-nml/patrist	https://github.com/phac-nml/galaxy_tools/tree/master/tools/patrist	0.1.2	python		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+peakachu	3109.0	78.0	peakachu	PEAKachu is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	peakachu	rnateam	https://github.com/tbischler/PEAKachu	https://github.com/bgruening/galaxytools/tree/master/tools/peakachu	0.2.0+galaxy1	peakachu	0.2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+pep_pointer	498.0	9.0	pep_pointer	PepPointer categorizes peptides by their genomic coordinates.								To update		Genomic Interval Operations, Proteomics	pep_pointer	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer	0.1.3+galaxy1	python		(1/1)	(1/1)	(1/1)	(0/1)	True	False
+pepquery	4862.0	23.0	pepquery	A peptide-centric MS search engine for novel peptide identification and validation.								To update	https://pepquery.org	Proteomics	pepquery	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery	1.6.2	pepquery	2.0.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+pepquery2	707.0	10.0	pepquery2, pepquery2_index, pepquery2_show_sets	PepQuery2 peptide-centric MS search for peptide identification and validation								Up-to-date	https://pepquery.org	Proteomics	pepquery2	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2	2.0.2	pepquery	2.0.2	(0/3)	(0/3)	(3/3)	(0/3)	True	False
+peptide_genomic_coordinate	468.0	9.0	peptide_genomic_coordinate	Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files								To update		Proteomics	peptide_genomic_coordinate	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptide_genomic_coordinate	1.0.0	python		(1/1)	(1/1)	(1/1)	(0/1)	True	False
+peptideshaker	17477.0	485.0	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI								To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.6	(4/4)	(4/4)	(4/4)	(4/4)	True	True
+peptimapper			peptimapper_clustqualify, peptimapper_clust_to_gff, peptimapper_pep_match, peptimapper_pep_novo_tag	Proteogenomics workflow for the expert annotation of eukaryotic genomes								To update	https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5431-9	Proteomics		genouest		https://github.com/genouest/galaxy-tools/tree/master/tools/peptimapper	2.0			(0/4)	(0/4)	(0/4)	(0/4)	True	False
+pepxml_to_xls				Convert PepXML to Tabular								To update		Proteomics	pepxml_to_xls	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepxml_to_xls				(0/1)	(0/1)	(0/1)	(0/1)	True	False
+percolator	368.0	5.0	batched_set_list_creator, percolator, percolator_input_converters, pout2mzid	Percolator								To update		Proteomics	percolator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/percolator	3.5	percolator	3.6.5	(0/4)	(4/4)	(4/4)	(0/4)	True	False
+pfamscan	165.0	19.0	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan		PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+pharokka	2565.0	74.0	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka		Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
+                pharokka
+            "		(0/1)	(1/1)	(1/1)	(0/1)	True	True
+phyloseq			phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq		phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	(0/4)	(0/4)	(4/4)	(0/4)	True	True
+phyml	1770.0	104.0	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml		PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408	(0/1)	(1/1)	(1/1)	(1/1)	True	True
+pi_db_tools			calc_delta_pi, pi_db_split, pi_dbspec_align	HiRIEF tools								To update		Proteomics	hirieftools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pi_db_tools	1.3	python		(0/3)	(0/3)	(0/3)	(0/3)	True	False
+picrust			picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust		PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	(0/6)	(6/6)	(5/6)	(6/6)	True	True
+picrust2			picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions	PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States	picrust2	picrust2		PICRUSt2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	To update	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.1	picrust2	2.5.2	(0/7)	(7/7)	(7/7)	(0/7)	True	True
+pipmir	275.0	21.0	pipmir	A method to identify novel plant miRNA.								To update	https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/	RNA	pipmir	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir	0.1.0	pipmir	1.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+piranha	1809.0	39.0	piranha	Piranha is a peak-caller for CLIP- and RIP-Seq data								To update		Sequence Analysis, RNA	piranha	rnateam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha	https://github.com/bgruening/galaxytools/tree/master/tools/piranha	1.2.1.0	piranha	1.2.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+plasflow	22589.0	278.0	PlasFlow	PlasFlow - Prediction of plasmid sequences in metagenomic contigs.	plasflow	plasflow		PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.	Sequence analysis	Metagenomics	Up-to-date	https://github.com/smaegol/PlasFlow	Sequence Analysis	plasflow	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow	1.1.0	plasflow	1.1.0	(1/1)	(1/1)	(1/1)	(0/1)	True	True
+plasmid_profiler_suite				Plasmid Profiler suite defining all dependencies for Plasmid Profiler								To update		Sequence Analysis	suite_plasmid_profiler	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmid_profiler_suite				(0/1)	(0/1)	(0/1)	(0/1)	True	False
+plasmidfinder	22.0	8.0	plasmidfinder	"""PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage"""	PlasmidFinder	PlasmidFinder		PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	Up-to-date	https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/	Sequence Analysis	plasmidfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder	2.1.6	plasmidfinder	2.1.6	(0/1)	(0/1)	(1/1)	(1/1)	True	True
+plasmidspades			plasmidspades	Genome assembler for assemblying plasmid								To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	3.15.5	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+platypus			bg_platypus	efficient and accurate variant-detection in high-throughput sequencing data								To update	http://www.well.ox.ac.uk/platypus	Sequence Analysis	platypus	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	https://github.com/bgruening/galaxytools/tree/master/tools/platypus	0.0.11	platypus		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+plotly_ml_performance_plots	1323.0	71.0	plotly_ml_performance_plots	performance plots for machine learning problems								To update	http://scikit-learn.org/stable/modules/classes.html#module-sklearn.metrics	Visualization	plotly_ml_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_ml_performance_plots	0.3	galaxy-ml	0.10.0	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+plotly_parallel_coordinates_plot	652.0	37.0	plotly_parallel_coordinates_plot	parallel coordinates plot produced with plotly								To update	https://plot.ly/python/parallel-coordinates-plot/	Visualization	plotly_parallel_coordinates_plot	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_parallel_coordinates_plot	0.2	python		(1/1)	(1/1)	(1/1)	(0/1)	True	False
+plotly_regression_performance_plots	843.0	79.0	plotly_regression_performance_plots	performance plots for regression problems								To update	http://scikit-learn.org/stable/supervised_learning.html#supervised-learning	Visualization	plotly_regression_performance_plots	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots	0.1	python		(1/1)	(1/1)	(1/1)	(0/1)	True	False
+pmd_fdr			pmd_fdr	Calculate Precursor Mass Discrepancy (PMD) for MS/MS								To update	https://github.com/slhubler/PMD-FDR-for-Galaxy-P	Proteomics	pmd_fdr	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr	1.4.0	r-base		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+poisson2test	116.0	6.0	poisson2test	Poisson two-sample test								To update	https://bitbucket.org/natefoo/taxonomy	Statistics, Metagenomics	poisson2test	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/poisson2test	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/poisson2test	1.0.0	taxonomy	0.10.0	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+polypolish	239.0	24.0	polypolish	"""Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix."""	Polypolish	Polypolish		Polypolish	Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	To update	https://github.com/rrwick/Polypolish	Sequence Analysis	polypolish	iuc	https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish	0.5.0	polypolish	0.6.0	(0/1)	(0/1)	(1/1)	(1/1)	True	True
+predictnls			predictnls	Python reimplementation of predictNLS for Galaxy								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	Sequence Analysis	predictnls	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	https://github.com/peterjc/pico_galaxy/tree/master/tools/predictnls	0.0.10			(0/1)	(0/1)	(0/1)	(0/1)	True	False
+presto			presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3	pRESTO toolkit for immune repertoire analysis.	presto	presto		pRESTO	Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires.	Nucleic acid sequence analysis	Sequencing, DNA, Immunology	To update	https://presto.readthedocs.io/	Sequence Analysis	presto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto	0.6.2	presto	0.7.2	(11/11)	(0/11)	(0/11)	(0/11)	True	False
+pretext			pretext_graph, pretext_map, pretext_snapshot	Process genome contacts maps processing images.								Up-to-date	https://github.com/wtsi-hpag/PretextSnapshot	Sequence Analysis	suite_pretext	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext	0.0.6	pretextgraph	0.0.6	(3/3)	(2/3)	(3/3)	(0/3)	True	False
+prinseq	7881.0	70.0	prinseq	PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets	prinseq	prinseq		PRINSEQ	PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions.	Read pre-processing, Sequence trimming, Sequence contamination filtering	Transcriptomics, Metagenomics, Genomics	To update	http://prinseq.sourceforge.net/manual.html	Fastq Manipulation, Metagenomics	prinseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq	@TOOL_VERSION+galaxy2	prinseq	0.20.4	(1/1)	(0/1)	(1/1)	(1/1)	True	False
+probecoverage			probecoverage	computes and plots read coverage of genomic regions by sequencing datasets								To update	http://artbio.fr	Sequence Analysis, Genomic Interval Operations, Graphics, Statistics	probecoverage	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	https://github.com/ARTbio/tools-artbio/tree/main/tools/probecoverage	0.22.0	pysam	0.22.1	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+prodigal			prodigal	A protein-coding gene prediction software tool for bacterial and archaeal genomes	prodigal	prodigal		Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes.	Genome annotation	Genomics, Sequence analysis	Up-to-date	https://github.com/hyattpd/Prodigal	Genome annotation	prodigal	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal	2.6.3	prodigal	2.6.3	(0/1)	(0/1)	(1/1)	(1/1)	True	True
+progressivemauve	1734.0	286.0	progressivemauve, xmfa2gff3	Mauve/ProgressiveMauve Multiple Sequence Aligner								To update		Sequence Analysis	progressivemauve	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve	https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve		progressivemauve	snapshot_2015_02_13	(2/2)	(0/2)	(2/2)	(0/2)	True	False
+prokka	371445.0	3233.0	prokka	Rapid annotation of prokaryotic genomes	prokka	prokka		Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.	Gene prediction, Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	Up-to-date	http://github.com/tseemann/prokka	Sequence Analysis	prokka	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka	1.14.6	prokka	1.14.6	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+promer			promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them								To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python		(0/1)	(0/1)	(0/1)	(0/1)	True	True
+prot-scriber			prot_scriber	Protein annotation of short human readable descriptions								To update	https://github.com/usadellab/prot-scriber	Proteomics	prot_scriber	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber	https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber	0.1.4	prot-scriber	0.1.5	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+protease_prediction	149.0	4.0	eden_protease_prediction	This tool can learn the cleavage specificity of a given class of proteases.								To update	https://github.com/fabriziocosta/eden	Sequence Analysis, Proteomics	protease_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/protease_prediction	0.9	eden	2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+protein_analysis			promoter2, Psortb, rxlr_motifs, signalp3, tmhmm2, wolf_psort	TMHMM, SignalP, Promoter, RXLR motifs, WoLF PSORT and PSORTb								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	Sequence Analysis	tmhmm_and_signalp	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	https://github.com/peterjc/pico_galaxy/tree/master/tools/protein_analysis	0.0.13	promoter		(0/6)	(0/6)	(6/6)	(0/6)	True	False
+protein_properties	256.0	15.0	bg_protein_properties	Calculation of various properties from given protein sequences								To update		Sequence Analysis	protein_properties	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	https://github.com/bgruening/galaxytools/tree/master/tools/protein_properties	0.2.0	biopython	1.70	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+proteinortho	2092.0	125.0	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho		Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	Up-to-date	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.1	(0/3)	(0/3)	(3/3)	(0/3)	True	True
+proteomiqon_joinquantpepionswithproteins	366.0	4.0	proteomiqon_joinquantpepionswithproteins	The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification.								To update	https://csbiology.github.io/ProteomIQon/tools/JoinQuantPepIonsWithProteins.html	Proteomics	proteomiqon_joinquantpepionswithproteins	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_joinquantpepionswithproteins	0.0.1	proteomiqon-joinquantpepionswithproteins	0.0.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+proteomiqon_labeledproteinquantification	14.0	5.0	proteomiqon_labeledproteinquantification	The tool LabeledProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabeledProteinQuantification.html	Proteomics	proteomiqon_labeledproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labeledproteinquantification	0.0.1	proteomiqon-labeledproteinquantification	0.0.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+proteomiqon_labelfreeproteinquantification	6.0	3.0	proteomiqon_labelfreeproteinquantification	The tool LabelFreeProteinQuantification estimates protein abundances using quantified peptide ions.								To update	https://csbiology.github.io/ProteomIQon/tools/LabelfreeProteinQuantification.html	Proteomics	proteomiqon_labelfreeproteinquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_labelfreeproteinquantification	0.0.1	proteomiqon-labelfreeproteinquantification	0.0.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+proteomiqon_mzmltomzlite	721.0	5.0	proteomiqon_mzmltomzlite	The tool MzMLToMzLite allows to convert mzML files to mzLite files.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/MzMLToMzLite.html	Proteomics	proteomiqon_mzmltomzlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomIQon_MzMLToMzLite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_mzmltomzlite	0.0.8	proteomiqon-mzmltomzlite	0.0.8	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+proteomiqon_peptidedb	96.0	6.0	proteomiqon_peptidedb	The tool ProteomIQon PeptideDB creates a peptide database in the SQLite format.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html	Proteomics	proteomiqon_peptidedb	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidedb	0.0.7	proteomiqon-peptidedb	0.0.7	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+proteomiqon_peptidespectrummatching	686.0	4.0	proteomiqon_peptidespectrummatching	Given raw an MS run in the mzLite format, this tool iterates across all MS/MS scans, determines precursor charge states and possible peptide spectrum matches using reimplementations of SEQUEST,Andromeda and XTandem.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html	Proteomics	proteomiqon_peptidespectrummatching	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching	0.0.7	proteomiqon-peptidespectrummatching	0.0.7	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+proteomiqon_proteininference	89.0	4.0	proteomiqon_proteininference	MS-based shotgun proteomics estimates protein abundances using a proxy: peptides. The process of 'Protein Inference' is concerned with the mapping of identified peptides to the proteins they putatively originated from.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/ProteinInference.html	Proteomics	proteomiqon_proteininference	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_proteininference	0.0.7	proteomiqon-proteininference	0.0.7	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+proteomiqon_psmbasedquantification	604.0	4.0	proteomiqon_psmbasedquantification	The PSMBasedQuantification tool was designed to allow label-free quantification as well as quantification of full metabolic labeled samples.								To update	https://csbiology.github.io/ProteomIQon/tools/PSMBasedQuantification.html	Proteomics	proteomiqon_psmbasedquantification	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmbasedquantification	0.0.8	proteomiqon-psmbasedquantification	0.0.9	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+proteomiqon_psmstatistics	694.0	4.0	proteomiqon_psmstatistics	The PSMStatistics tool utilizes semi supervised machine learning techniques to integrate search engine scores as well as the mentioned quality scores into one single consensus score.								Up-to-date	https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html	Proteomics	proteomiqon_psmstatistics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_psmstatistics	0.0.8	proteomiqon-psmstatistics	0.0.8	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+proteore_venn_diagram	15.0		proteore_venn_diagram	ProteoRE JVenn Diagram								To update		Proteomics	proteore_venn_diagram	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteore_venn_diagram	2021.06.08	python		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+pseudogenome			pseudogenome	Create a pseudogenome from a multiple fasta file either with a JCVI linker or custom length and characters.								To update	https://github.com/phac-nml/galaxy_tools	Sequence Analysis	pseudogenome	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/pseudogenome	1.0.0	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+psm2sam			PSMtoSAM	PSM to SAM								To update	https://bioconductor.org/packages/release/bioc/html/proBAMr.html	Proteomics	psm_to_sam	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/probam_suite/psm2sam	1.3.2.1	r-base		(0/1)	(0/1)	(0/1)	(1/1)	True	False
+psm_validation	20.0		psmvalidator	Validate PSM from Ion Fragmentation								To update	https://github.com/galaxyproteomics/psm_fragments.git	Proteomics	psm_validation	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation	1.0.3			(0/1)	(0/1)	(1/1)	(0/1)	True	False
+psy-maps			psy_maps	Visualization of regular geographical data on a map with psyplot								To update	https://github.com/Chilipp/psy-maps	Visualization, Climate Analysis	psy_maps	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps	1.2.1	python		(0/1)	(0/1)	(1/1)	(0/1)	True	False
+pureclip	1423.0	36.0	pureclip	PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data								To update	https://github.com/skrakau/PureCLIP	Sequence Analysis, RNA, CLIP-seq	pureclip	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pureclip	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip	1.0.4	pureclip	1.3.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+purge_dups	16800.0	167.0	purge_dups	Purge haplotigs and overlaps in an assembly based on read depth	purge_dups	purge_dups		purge_dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences	Genome assembly, Read binning, Scaffolding	Sequence assembly	Up-to-date	https://github.com/dfguan/purge_dups	Assembly	purge_dups	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups	https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups	1.2.6	purge_dups	1.2.6	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+pycoqc	21123.0	350.0	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc		pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+pygenometracks	11332.0	377.0	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks		pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+pyprophet			pyprophet_export, pyprophet_merge, pyprophet_peptide, pyprophet_protein, pyprophet_score, pyprophet_subsample	Semi-supervised learning and scoring of OpenSWATH results.								To update	https://github.com/PyProphet/pyprophet	Proteomics		galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet	2.1.4	pyprophet	2.2.5	(0/6)	(4/6)	(6/6)	(0/6)	True	False
+pysradb			pysradb_search	pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria.	pysradb	pysradb		pysradb	Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive.	Deposition, Data retrieval	Sequencing, Gene transcripts, Bioinformatics	To update	https://github.com/saketkc/pysradb	Sequence Analysis	pysradb_search	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb	1.4.2	pysradb	2.2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+pyteomics			mztab2tsv	Tools using the pyteomics library	pyteomics	pyteomics		Pyteomics	Framework for proteomics data analysis, supporting mzML, MGF, pepXML and more.	Protein identification	Proteomics, Proteomics experiment	To update	https://pyteomics.readthedocs.io/en/latest/	Proteomics, Metabolomics	pyteomics	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics	4.4.1	pyteomics	4.7.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+qiime_add_on			qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_add_on		qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	(0/2)	(0/2)	(2/2)	(2/2)	True	True
+qiime_core			qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis								To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	(0/32)	(0/32)	(32/32)	(32/32)	True	True
+qq_tools			qq_manhattan									To update	https://CRAN.R-project.org/package=qqman	Visualization, Variant Analysis		iuc		https://github.com/galaxyproject/tools-iuc/tree/main/tools/qq_tools	0.1.0	r-qqman	0.1.4	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+qualimap			qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq		qualimap	qualimap		QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	To update	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.2.2d	qualimap	2.3	(4/4)	(4/4)	(4/4)	(1/4)	True	True
+quality_filter			qualityFilter	Filter nucleotides based on quality scores								To update		Sequence Analysis, Variant Analysis	quality_filter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/quality_filter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/quality_filter	1.0.1	bx-python	0.11.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+quantp	230.0	6.0	quantp	Correlation between protein and transcript abundance								To update		Proteomics	quantp	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantp	1.1.2	r-data.table	1.11.6	(0/1)	(0/1)	(1/1)	(1/1)	True	False
+quantwiz_iq	32.0	1.0	quantwiz_iq	Isobaric Quantitation using QuantWiz-IQ								Up-to-date	https://sourceforge.net/projects/quantwiz/	Proteomics	quantwiz_iq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/quantwiz_iq	2.0	quantwiz-iq	2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+quasitools			aacoverage, aavariants, callcodonvar, callntvar, complexity_bam, complexity_fasta, consensus, distance, dnds, drmutations, hydra, quality	A collection of tools for analysing Viral Quasispecies								Up-to-date	https://github.com/phac-nml/quasitools	Sequence Analysis	quasitools	nml	https://github.com/phac-nml/quasitools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/quasitools	0.7.0	quasitools	0.7.0	(0/12)	(12/12)	(0/12)	(12/12)	True	False
+quast	51567.0	3567.0	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast		QUAST	QUAST stands for QUality ASsessment Tool.  It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+quickmerge			quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge		quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+rRNA			meta_rna	Identification of ribosomal RNA genes in metagenomic fragments.								To update	http://weizhong-lab.ucsd.edu/meta_rna/	RNA	rrna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rRNA	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA	0.1	hmmsearch3.0		(0/1)	(0/1)	(0/1)	(0/1)	True	True
+racon	21353.0	309.0	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon		Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+ragtag	2833.0	237.0	ragtag	Reference-guided scaffolding of draft genomes tool.	ragtag	ragtag		ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/malonge/RagTag	Assembly	ragtag	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag	2.1.0	ragtag	2.1.0	(0/1)	(0/1)	(1/1)	(1/1)	True	False
+rapidnj	176.0	14.0	rapidnj	Galaxy wrapper for the RapidNJ tool	rapidnj	rapidnj		RapidNJ	A tool for fast canonical neighbor-joining tree construction.	Phylogenetic tree generation	Phylogeny	Up-to-date	https://birc.au.dk/software/rapidnj/	Phylogenetics	rapidnj	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rapidnj	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj	2.3.2	rapidnj	2.3.2	(1/1)	(0/1)	(1/1)	(1/1)	True	False
+rasusa			rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa		rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	0.8.0	rasusa	2.0.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+raven	6902.0	262.0	raven	Raven is a de novo genome assembler for long uncorrected reads.								To update	https://github.com/lbcb-sci/raven	Assembly		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raven	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven	1.8.0	raven-assembler	1.8.3	(0/1)	(1/1)	(1/1)	(1/1)	True	False
+rawtools	175.0	14.0	rawtools	Raw Tools								To update	https://github.com/kevinkovalchik/RawTools	Proteomics	rawtools	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/rawtools		rawtools	2.0.4	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+raxml	6808.0	383.0	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml		RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+rbpbench	36.0		rbpbench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs	rbpbench	rbpbench		RBPBench	Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs		RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis	Up-to-date	https://github.com/michauhl/RBPBench	Sequence Analysis, RNA, CLIP-seq	rbpbench	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench	0.8.1	rbpbench	0.8.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+rcas	1226.0	38.0	rcas	RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments								To update	https://github.com/BIMSBbioinfo/RCAS	RNA	rcas	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas	1.5.4	bioconductor-rcas	1.28.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+rcve			rcve1	Compute RCVE								To update		Sequence Analysis, Variant Analysis	rcve	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/rcve	https://github.com/galaxyproject/tools-devteam/tree/main/tools/rcve	1.0.0	R		(1/1)	(0/1)	(0/1)	(0/1)	True	False
+read_it_and_keep	3370.0	71.0	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep		read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+reago			reago	Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.	reago	reago		REAGO	This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	Up-to-date	https://github.com/chengyuan/reago-1.1	Metagenomics, RNA	reago	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago	1.1	reago	1.1	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+recentrifuge	331.0	48.0	recentrifuge	"""With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."""	Recentrifuge	Recentrifuge		Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.14.0	recentrifuge	1.14.0	(0/1)	(0/1)	(1/1)	(1/1)	True	True
+red	578.0	88.0	red	Red (REpeat Detector)	red	red		RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.	RNA-Seq analysis, Editing	RNA, Sequencing, Data visualisation	Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	https://github.com/galaxyproject/tools-iuc/tree/main/tools/red	2018.09.10	red	2018.09.10	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+refseq_masher			refseq_masher_contains, refseq_masher_matches	Find what genomes match or are contained within your sequence data using Mash_ and a Mash sketch database.								Up-to-date	https://github.com/phac-nml/refseq_masher	Sequence Analysis	refseq_masher	nml	https://github.com/phac-nml/refseq_masher	https://github.com/phac-nml/galaxy_tools/tree/master/tools/refseq_masher	0.1.2	refseq_masher	0.1.2	(0/2)	(0/2)	(0/2)	(2/2)	True	False
+regionalgam			regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend									To update	https://github.com/RetoSchmucki/regionalGAM	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam	1.5	r-mgcv		(0/7)	(0/7)	(7/7)	(7/7)	True	False
+remurna	42.0	2.0	remurna	remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation								To update	https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna	RNA	remurna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna	1.0.0	remurna	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+repeat_masker	3750.0	248.0	repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.								To update	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	https://github.com/bgruening/galaxytools/tree/master/tools/repeat_masker	0.1.2	RepeatMasker	4.1.5	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+repeatexplorer2			repeatexplorer_clustering	Tool for annotation of repeats from unassembled shotgun reads.								To update	https://github.com/repeatexplorer/repex_tarean	Genome annotation	repeatexplorer2	gga	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2	2.3.8			(0/1)	(0/1)	(1/1)	(0/1)	True	True
+repeatmasker			repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	repeatmasker	repeatmasker		RepeatMasker	A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).	Genome annotation	Sequence analysis, Sequence composition, complexity and repeats	Up-to-date	http://www.repeatmasker.org/	Sequence Analysis	repeat_masker	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker	4.1.5	repeatmasker	4.1.5	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+repeatmodeler	1177.0	217.0	repeatmodeler	RepeatModeler - Model repetitive DNA	repeatmodeler	repeatmodeler		RepeatModeler	De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats.	Repeat sequence detection	Sequence composition, complexity and repeats, Sequence composition, complexity and repeats	To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler	2.0.5			(1/1)	(1/1)	(1/1)	(1/1)	True	False
+revoluzer			revoluzer_crex, revoluzer_distmat	revoluzer wrappers	revoluzer	revoluzer		revoluzer	Various tools for genome rearrangement analysis. CREx, TreeREx, etc	Structural variation detection	Molecular evolution, Phylogeny	Up-to-date	https://gitlab.com/Bernt/revoluzer/	Phylogenetics	revoluzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer	0.1.6	revoluzer	0.1.6	(0/2)	(0/2)	(2/2)	(0/2)	True	False
+ribotaper	628.0	44.0	ribotaper_create_annotation, ribotaper_create_metaplots, ribotaper_ribosome_profiling	A method for defining traslated ORFs using Ribosome Profiling data.	ribotaper	ribotaper		RiboTaper	New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.	Gene expression profiling	Functional genomics	To update	https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/	RNA	ribotaper	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/ribotaper	1.3.1a	ribotaper	1.3.1	(0/3)	(0/3)	(3/3)	(0/3)	True	False
+ribowaltz			ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	riboWaltz	riboWaltz		riboWaltz	riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data.		Computational biology	To update	https://github.com/LabTranslationalArchitectomics/riboWaltz	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz	1.2.0	ribowaltz	2.0	(0/2)	(0/2)	(2/2)	(0/2)	True	False
+rna_shapes			RNAshapes	Compute secondary structures of RNA								To update		RNA	rnashapes	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rna_shapes	3.3.0	@EXECUTABLE@		(0/1)	(0/1)	(1/1)	(0/1)	True	False
+rnabob	164.0	3.0	rbc_rnabob	Fast pattern searching for RNA structural motifs								To update	http://eddylab.org/software.html	RNA	rnabob	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnabob	2.2.1.0	rnabob	2.2.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+rnacode	1358.0	5.0	rbc_rnacode	Analyze the protein coding potential in MSA								To update		RNA	rnacode	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacode	0.3.2	rnacode	0.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+rnacommender	1074.0	6.0	rbc_rnacommender	RNAcommender is a tool for genome-wide recommendation of RNA-protein interactions.								To update	https://github.com/gianlucacorrado/RNAcommender	RNA	rnacommender	rnateam	https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnacommender	0.1.1	sam	3.5	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+rnalien	33.0	4.0	RNAlien	RNAlien unsupervized RNA family model construction								To update	http://rna.tbi.univie.ac.at/rnalien/	RNA, Sequence Analysis	rnalien	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnalien	1.3.6	rnalien	1.8.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+rnaquast	1110.0	109.0	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	rnaQUAST	rnaQUAST		rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.	De-novo assembly, Transcriptome assembly, Sequence assembly validation	Sequence assembly, Transcriptomics, RNA-seq	Up-to-date	https://github.com/ablab/rnaquast	Assembly, RNA	rnaquast	iuc	https://git.ufz.de/lehmanju/rnaquast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast	2.2.3	rnaquast	2.2.3	(1/1)	(0/1)	(1/1)	(1/1)	True	False
+rnasnp	86.0	5.0	rnasnp	RNAsnp Efficient detection of local RNA secondary structure changes induced by SNPs								To update	http://rth.dk/resources/rnasnp/	RNA	rnasnp	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rnasnp	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnasnp	1.2.0	rnasnp	1.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+rnaz	42965.0	14.0	rnaz, rnaz_annotate, rnaz_cluster, rnaz_randomize_aln, rnaz_select_seqs, rnaz_window	RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments.								Up-to-date	https://www.tbi.univie.ac.at/~wash/RNAz/	RNA	rnaz	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaz	2.1.1	rnaz	2.1.1	(0/6)	(0/6)	(6/6)	(0/6)	True	False
+roary	12225.0	656.0	roary	Roary the pangenome pipeline	roary	roary		Roary	A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.	Genome assembly	DNA, Genomics, Mapping	Up-to-date	https://sanger-pathogens.github.io/Roary/	Sequence Analysis	roary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary	3.13.0	roary	3.13.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+rsem	2273.0	199.0	extract_transcript_to_gene_map_from_trinity, purgegtffrommultichromgenes, rsembowtie2, rsembowtie	transcript quantification from RNA-Seq data								To update	https://github.com/deweylab/RSEM	Transcriptomics, RNA	rsem	artbio	https://github.com/artbio/tools-artbio/tree/master/tools/rsem	https://github.com/ARTbio/tools-artbio/tree/main/tools/rsem		rsem	1.3.3	(0/4)	(0/4)	(1/4)	(0/4)	True	False
+rseqc	135036.0	3269.0	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc		RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	(22/22)	(22/22)	(22/22)	(22/22)	True	True
+ruvseq	1236.0	76.0	ruvseq	Remove Unwanted Variation from RNA-Seq Data	ruvseq	ruvseq		RUVSeq	This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.	Differential gene expression analysis	Gene expression, RNA-seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	ruvseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq	1.26.0	bioconductor-ruvseq	1.36.0	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+sailfish	4024.0	55.0	sailfish	Sailfish is a tool for transcript quantification from RNA-seq data								To update	http://www.cs.cmu.edu/~ckingsf/software/sailfish/	Sequence Analysis, RNA	sailfish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	https://github.com/bgruening/galaxytools/tree/master/tools/sailfish	0.10.1.1	bzip2		(1/1)	(1/1)	(1/1)	(1/1)	True	False
+salmon	55161.0	746.0	alevin, salmon, salmonquantmerge	Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data.	salmon	salmon		Salmon	A tool for transcript expression quantification from RNA-seq data	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Gene expression, Transcriptomics	To update	https://github.com/COMBINE-lab/salmon	Sequence Analysis, RNA, Transcriptomics		bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	https://github.com/bgruening/galaxytools/tree/master/tools/salmon	1.10.1	salmon	1.10.3	(2/3)	(1/3)	(3/3)	(1/3)	True	True
+salmon-kallisto-mtx-to-10x			_salmon_kallisto_mtx_to_10x	Transforms .mtx matrix and associated labels into a format compatible with tools expecting old-style 10X data								To update	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary	Sequence Analysis	salmon_kallisto_mtx_to_10x	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x/.shed.yml	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/salmon-kallisto-mtx-to-10x	0.0.1+galaxy6	scipy		(1/1)	(1/1)	(1/1)	(0/1)	True	False
+salsa2			salsa	A tool to scaffold long read assemblies with Hi-C	SALSA	SALSA		SALSA	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly, DNA binding sites, Mapping	Up-to-date	https://github.com/marbl/SALSA	Assembly	salsa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/salsa2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2	2.3	salsa2	2.3	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+sample_seqs	3765.0	149.0	sample_seqs	Sub-sample sequences files (e.g. to reduce coverage)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	Assembly, Fasta Manipulation, Fastq Manipulation, Sequence Analysis	sample_seqs	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	https://github.com/peterjc/pico_galaxy/tree/master/tools/sample_seqs	0.2.6	biopython	1.70	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+samtools_depad			samtools_depad	Re-align a SAM/BAM file with a padded reference (using samtools depad)								To update	http://www.htslib.org/	Assembly, SAM, Sequence Analysis	samtools_depad	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depad	0.0.5	samtools	1.20	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+samtools_depth	4948.0	296.0	samtools_depth	Coverage depth via samtools								To update	http://www.htslib.org/	Assembly, Sequence Analysis, SAM	samtools_depth	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_depth	0.0.3	samtools	1.20	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+samtools_idxstats	48426.0	1450.0	samtools_idxstats	BAM mapping statistics (using samtools idxstats)								To update	http://www.htslib.org/	Assembly, Next Gen Mappers, SAM	samtools_idxstats	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats	0.0.6	samtools	1.20	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+sarscov2formatter	173.0	7.0	sarscov2formatter	sarscov2formatter custom script								Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+sarscov2summary	140.0	1.0	sarscov2summary	sarscov2summary custom script								To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+sashimi_plot			sashimi_plot	Generates a sashimi plot from bam files.								To update	http://artbio.fr	RNA, Transcriptomics, Graphics, Visualization	sashimi_plot	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sashimi_plot	https://github.com/ARTbio/tools-artbio/tree/main/tools/sashimi_plot	0.1.1	python		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+sc3			sc3_calc_biology, sc3_calc_consens, sc3_calc_dists, sc3_calc_transfs, sc3_estimate_k, sc3_kmeans, sc3_prepare	De-composed SC3 functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-sc3-scripts and SC3 1.8.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_sc3	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/sc3	1.8.0	sc3-scripts	0.0.6	(0/7)	(0/7)	(7/7)	(0/7)	True	False
+scanpy			anndata_ops, scanpy_filter_cells, scanpy_filter_genes, scanpy_find_cluster, scanpy_find_markers, scanpy_find_variable_genes, scanpy_integrate_bbknn, scanpy_integrate_combat, scanpy_integrate_harmony, scanpy_integrate_mnn, scanpy_plot_scrublet, scanpy_multiplet_scrublet, scanpy_compute_graph, scanpy_normalise_data, scanpy_parameter_iterator, scanpy_plot_embed, scanpy_plot_trajectory, scanpy_read_10x, scanpy_regress_variable, scanpy_run_diffmap, scanpy_run_dpt, scanpy_run_fdg, scanpy_run_paga, scanpy_run_pca, scanpy_run_tsne, scanpy_run_umap, scanpy_scale_data	scanpy-scripts, command-line wrapper scripts around Scanpy.								To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis, RNA	scanpy_scripts	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy	1.9.3	scanpy-scripts	1.9.301	(17/27)	(27/27)	(27/27)	(0/27)	True	False
+scanpy			scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders	Scanpy – Single-Cell Analysis in Python	scanpy	scanpy		SCANPY	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.	Differential gene expression analysis	Gene expression, Cell biology, Genetics	To update	https://scanpy.readthedocs.io	Transcriptomics, Sequence Analysis	scanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy	1.9.6	scanpy	1.7.2	(6/6)	(6/6)	(6/6)	(0/6)	True	False
+scater			scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne	Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization.	scater	scater		scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.	Read pre-processing, Sequencing quality control, Sequence visualisation	RNA-seq, Quality affairs, Molecular genetics	To update	http://bioconductor.org/packages/scater/	Transcriptomics, RNA, Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater	1.22.0	bioconductor-scater	1.30.1	(0/5)	(5/5)	(5/5)	(0/5)	True	False
+scater			scater_calculate_cpm, scater_calculate_qc_metrics, scater_filter, scater_is_outlier, scater_normalize, scater_read_10x_results	De-composed Scater functionality tools, based on https://github.com/ebi-gene-expression-group/bioconductor-scater-scripts and Scater 1.8.4.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scater	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scater	1.10.0	scater-scripts	0.0.5	(0/6)	(1/6)	(6/6)	(0/6)	True	False
+schicexplorer			schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol	scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data.								To update	https://github.com/joachimwolff/schicexplorer	Sequence Analysis, Transcriptomics, Visualization	schicexplorer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer	4	schicexplorer	7	(0/16)	(0/16)	(16/16)	(0/16)	True	False
+scikit-bio			scikit_bio_diversity_beta_diversity	scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics								Up-to-date	http://scikit-bio.org/	Sequence Analysis	scikit_bio	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scikit_bio	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio	0.4.2	scikit-bio	0.4.2	(1/1)	(0/1)	(0/1)	(0/1)	True	False
+scmap			scmap_get_std_output, scmap_index_cell, scmap_index_cluster, scmap_preprocess_sce, scmap_scmap_cell, scmap_scmap_cluster, scmap_select_features	De-composed scmap functionality tools, based on https://github.com/ebi-gene-expression-group/scmap-cli and scmap 1.6.0.								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scmap	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scmap	1.6.4	scmap-cli	0.1.0	(0/7)	(0/7)	(7/7)	(0/7)	True	False
+scoary	676.0	61.0	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary		Scoary	Pan-genome wide association studies and  is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+scpipe	628.0	11.0	scpipe	A flexible preprocessing pipeline for single-cell RNA-sequencing data	scpipe	scpipe		scPipe	A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.	Genome annotation, Validation, Alignment, Visualisation	Gene expression, RNA-Seq, Sequencing	To update	http://bioconductor.org/packages/release/bioc/html/scPipe.html	Transcriptomics, RNA, Statistics	scpipe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe	1.0.0+galaxy2	bioconductor-scpipe	2.2.0	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+scpred			scpred_get_feature_space, scpred_get_std_output, scpred_predict_labels, scpred_train_model	De-composed scPred functionality tools, see https://github.com/ebi-gene-expression-group/scpred-cli and r-scPred 1.0								To update		Transcriptomics, RNA, Statistics, Sequence Analysis	suite_scpred	ebi-gxa	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scpred	1.0.2	scpred-cli	0.1.0	(0/4)	(0/4)	(4/4)	(0/4)	True	False
+sdmpredictors			sdmpredictors_list_layers	Terrestrial and marine predictors for species distribution modelling.								To update	https://cran.r-project.org/web/packages/sdmpredictors/index.html	Ecology	sdmpredictors	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors	0.2.15	r-base		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+selectsequencesfrommsa	457.0	27.0	selectsequencesfrommsa	SelectSequences - selects representative entries from a multiple sequence alignment in clustal format								Up-to-date	https://github.com/eggzilla/SelectSequences	RNA, Sequence Analysis	selectsequencesfrommsa	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/selectsequencesfrommsa	1.0.5	selectsequencesfrommsa	1.0.5	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+semibin	183.0	10.0	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin		SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	(0/6)	(0/6)	(6/6)	(1/6)	True	True
+seq2hla	288.0	16.0	seq2hla	Precision HLA typing and expression from RNAseq data	seq2hla	seq2hla		Seq2HLA	seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class.	Read mapping, Genetic variation analysis	Transcriptomics, Mapping	Up-to-date	https://github.com/TRON-Bioinformatics/seq2HLA	Sequence Analysis	seq2hla	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla	2.3	seq2hla	2.3	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+seq_composition	874.0	71.0	seq_composition	Sequence composition								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	Sequence Analysis	seq_composition	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_composition	0.0.5	biopython	1.70	(1/1)	(0/1)	(1/1)	(1/1)	True	False
+seq_filter_by_id	25302.0	306.0	seq_filter_by_id	Filter sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_filter_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id	0.2.9	biopython	1.70	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+seq_filter_by_mapping	3784.0	82.0	seq_filter_by_mapping	Filter sequencing reads using SAM/BAM mapping files								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	Assembly, Fasta Manipulation, Fastq Manipulation, SAM, Sequence Analysis	seq_filter_by_mapping	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_mapping	0.0.8	biopython	1.70	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+seq_length			seq_length	Compute sequence length (from FASTA, QUAL, FASTQ, SFF, etc)								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	seq_length	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_length	0.0.5	biopython	1.70	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+seq_primer_clip			seq_primer_clip	Trim off 5' or 3' primers								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	Assembly, Fasta Manipulation, Text Manipulation	seq_primer_clip	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_primer_clip	0.0.18	galaxy_sequence_utils	1.1.5	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+seq_rename			seq_rename	Rename sequences with ID mapping from a tabular file								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_rename	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename	0.0.10	galaxy_sequence_utils	1.1.5	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+seq_select_by_id			seq_select_by_id	Select sequences by ID								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	Fasta Manipulation, Sequence Analysis, Text Manipulation	seq_select_by_id	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id	0.0.15	biopython	1.70	(0/1)	(1/1)	(0/1)	(0/1)	True	False
+seqcomplexity	68.0	16.0	seqcomplexity	Sequence complexity for raw reads								Up-to-date	https://github.com/stevenweaver/seqcomplexity	Sequence Analysis		iuc	https://github.com/stephenshank/tools-iuc/tree/seqcomplexity/tools/seqcomplexity/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity	0.1.2	seqcomplexity	0.1.2	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+seqkit			seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit		seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	To update	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.3.1	seqkit	2.8.1	(0/5)	(2/5)	(3/5)	(2/5)	True	True
+seqprep			seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep		SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+seqsero2	12.0		seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2		SeqSero2	"rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)"	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+seqtk	59668.0	753.0	seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq	Toolkit for processing sequences in FASTA/Q formats	seqtk	seqtk		seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.	Data handling, Sequence file editing	Data management	Up-to-date	https://github.com/lh3/seqtk	Sequence Analysis	seqtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk	1.4	seqtk	1.4	(15/15)	(15/15)	(15/15)	(15/15)	True	False
+seqtk_nml			seqtk_nml_sample	Tool to downsample fastq reads								To update	https://github.com/lh3/seqtk	Sequence Analysis	seqtk_nml	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/galaxy_tools/tree/master/tools/seqtk_nml	1.0.1	seqtk	1.4	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+seqwish	271.0		seqwish	Alignment to variation graph inducer								To update	https://github.com/ekg/seqwish	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish	0.7.5	seqwish	0.7.10	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+seurat	1543.0	66.0	seurat_convert, seurat_dim_plot, seurat_export_cellbrowser, seurat_filter_cells, seurat_find_clusters, seurat_find_markers, seurat_find_neighbours, seurat_find_variable_genes, seurat_hover_locator, seurat_integration, seurat_map_query, seurat_normalise_data, seurat_plot, seurat_read10x, seurat_run_pca, seurat_run_tsne, seurat_run_umap, seurat_scale_data, seurat_select_integration_features	De-composed Seurat functionality tools, based on https://github.com/ebi-gene-expression-group/r-seurat-scripts and Seurat 2.3.1								Up-to-date	https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/	Transcriptomics, RNA, Statistics, Sequence Analysis	suite_seurat	ebi-gxa		https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/seurat	4.0.0	seurat-scripts	4.0.0	(0/19)	(0/19)	(14/19)	(0/19)	True	False
+seurat	1543.0	66.0	seurat	A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data								To update	https://github.com/satijalab/seurat	Transcriptomics, RNA, Statistics	seurat	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat	4.3.0.1	r-seurat	3.0.2	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+shasta	763.0	154.0	shasta	Fast de novo assembly of long read sequencing data								To update	https://github.com/chanzuckerberg/shasta	Assembly, Nanopore	shasta	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta	0.6.0	shasta	0.11.1	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+shorah			shorah_amplicon	Reconstruct haplotypes using ShoRAH in amplicon mode	shorah	shorah		ShoRAH	Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	To update	https://github.com/cbg-ethz/shorah/blob/master/README.md	Sequence Analysis	shorah_amplicon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah	1.1.3	shorah	1.99.2	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+short_reads_figure_high_quality_length			hist_high_quality_score	Histogram of high quality score reads								To update		Sequence Analysis, Graphics	short_reads_figure_high_quality_length	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_high_quality_length	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_high_quality_length	1.0.0	rpy		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+short_reads_figure_score	163.0	13.0	quality_score_distribution	Build base quality distribution								To update		Sequence Analysis, Graphics	short_reads_figure_score	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/short_reads_figure_score	https://github.com/galaxyproject/tools-devteam/tree/main/tools/short_reads_figure_score	1.0.2	fontconfig		(0/1)	(0/1)	(1/1)	(0/1)	True	False
+shovill	41600.0	1008.0	shovill	Faster de novo assembly pipeline based around Spades	shovill	shovill		shovill	Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads.  Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too.	Genome assembly	Genomics, Microbiology, Sequence assembly	Up-to-date	https://github.com/tseemann/shovill	Assembly	shovill	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill	https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill	1.1.0	shovill	1.1.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+sickle	14982.0	269.0	sickle	A windowed adaptive trimming tool for FASTQ files using quality	sickle	sickle		sickle	A  tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads.	Sequence trimming	Data quality management	To update	https://github.com/najoshi/sickle	Fastq Manipulation, Sequence Analysis	sickle	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle	1.33.2	sickle-trim	1.33	(1/1)	(0/1)	(1/1)	(1/1)	True	False
+sina	1128.0	42.0	sina	SINA reference based multiple sequence alignment	sina	sina		SINA	Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment	Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment	Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy	Up-to-date	https://sina.readthedocs.io/en/latest/	Sequence Analysis	sina	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina	1.7.2	sina	1.7.2	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+sinto			sinto_barcode, sinto_fragments	Sinto single-cell analysis tools								To update	https://github.com/timoast/sinto	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto	0.9.0	sinto	0.10.0	(2/2)	(0/2)	(2/2)	(0/2)	True	False
+sistr_cmd	2489.0	133.0	sistr_cmd	SISTR in silico serotyping tool								To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2	(0/1)	(1/1)	(1/1)	(0/1)	True	True
+sixgill	293.0	24.0	sixgill_build, sixgill_filter, sixgill_makefasta, sixgill_merge	Six-frame Genome-Inferred Libraries for LC-MS/MS								Up-to-date		Proteomics, MetaProteomics	sixgill	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill	0.2.4	sixgill	0.2.4	(0/4)	(0/4)	(4/4)	(0/4)	True	False
+slamdunk	361.0	2.0	alleyoop, slamdunk	Slamdunk maps and quantifies SLAMseq reads								Up-to-date	http://t-neumann.github.io/slamdunk	RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers	slamdunk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk	0.4.3	slamdunk	0.4.3	(2/2)	(0/2)	(2/2)	(0/2)	True	False
+sleuth	64.0	8.0	sleuth	Sleuth is a program for differential analysis of RNA-Seq data.	sleuth	sleuth		sleuth	A statistical model and software application for RNA-seq differential expression analysis.	Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation	RNA-seq, Gene expression, Statistics and probability	Up-to-date	https://github.com/pachterlab/sleuth	Transcriptomics, RNA, Statistics	sleuth	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sleuth	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth	0.30.1	r-sleuth	0.30.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+small_rna_clusters			small_rna_clusters	clusters small rna reads in alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_clusters	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_clusters	1.3.0	pysam	0.22.1	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+small_rna_maps			small_rna_maps	Generates small read maps from alignment BAM files								To update	http://artbio.fr	RNA, SAM, Graphics, Next Gen Mappers	small_rna_maps	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_maps	3.1.1	numpy		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+small_rna_signatures			overlapping_reads, signature	Computes the tendency of small RNAs to overlap with each other.								To update	http://artbio.fr	RNA	small_rna_signatures	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures	https://github.com/ARTbio/tools-artbio/tree/main/tools/small_rna_signatures	3.4.2	pysam	0.22.1	(0/2)	(0/2)	(0/2)	(0/2)	True	False
+smallgenomeutilities			smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe		V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.0	smallgenomeutilities	0.4.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+smalt			smalt	SMALT aligns DNA sequencing reads with a reference genome.								Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+smart_domains			smart_domains	SMART domains								To update	http://smart.embl.de/	Sequence Analysis	smart_domains	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smart_domains	0.1.0	perl-bioperl	1.7.8	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+smudgeplot	203.0	22.0	smudgeplot	Inference of ploidy and heterozygosity structure using whole genome sequencing	smudgeplots	smudgeplots		Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568	Sequence trimming, Genotyping, k-mer counting	Sequence assembly, Genetic variation, Mathematics	Up-to-date	https://github.com/KamilSJaron/smudgeplot	Assembly	smudgeplot	galaxy-australia	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot	0.2.5	smudgeplot	0.2.5	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+snap			snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap		SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	(1/2)	(1/2)	(1/2)	(0/2)	True	True
+sniffles	919.0	58.0	sniffles	Galaxy wrapper for sniffles	sniffles	sniffles		Sniffles	An algorithm for structural variation detection from third generation sequencing alignment.	Sequence analysis, Structural variation detection	DNA structural variation, Sequencing	To update	https://github.com/fritzsedlazeck/Sniffles	Sequence Analysis	sniffles	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles	1.0.12	sniffles	2.3.3	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+snipit	669.0	22.0	snipit	Summarise snps relative to a reference sequence	snipit	snipit		snipit	Summarise snps relative to a reference sequence	Base position variability plotting	Virology	Up-to-date	https://github.com/aineniamh/snipit	Variant Analysis, Sequence Analysis	snipit	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit	1.2	snipit	1.2	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+snippy	105708.0	1372.0	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy		snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	(3/3)	(3/3)	(3/3)	(3/3)	True	True
+snv_matrix			snvmatrix	Generate matrix of SNV distances								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	snv_matrix	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/snv_matrix	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+socru	621.0	13.0	socru	Order and orientation of complete bacterial genomes								To update	https://github.com/quadram-institute-bioscience/socru	Sequence Analysis	socru	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/socru	https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru	2.1.7	socru	2.2.4	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+sonneityping	1.0	1.0	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping		sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+sortmerna	18504.0	376.0	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna		SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	Up-to-date	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.6	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+spades	58834.0	2309.0	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	coronaspades, rnaspades, metaspades, rnaviralspades, plasmidspades, metaviralspades, metaplasmidspades, spades, biosyntheticspades		SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	Up-to-date	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	3.15.5	(9/9)	(9/9)	(9/9)	(9/9)	True	True
+spaln	446.0	34.0	list_spaln_tables, spaln	Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.								To update	http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/	Sequence Analysis, Genome annotation	spaln	iuc	https://github.com/ogotoh/spaln	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln	2.4.9	python		(2/2)	(0/2)	(2/2)	(0/2)	True	False
+spatyper			spatyper	Determines SPA type based on repeats in a submitted staphylococcal protein A fasta file.								Up-to-date	https://github.com/HCGB-IGTP/spaTyper	Sequence Analysis	spatyper	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/spatyper	0.3.3	spatyper	0.3.3	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+spectrast2spectrast_irt			gp_spectrast2spectrast_irt	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2spectrast_irt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt	0.1.0	msproteomicstools	0.11.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+spectrast2tsv			gp_spectrast2tsv	Filter from spectraST files to swath input files								To update		Proteomics	spectrast2tsv	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2tsv	0.1.0	msproteomicstools	0.11.0	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+spocc			spocc_occ	Get species occurences data								To update	https://cran.r-project.org/web/packages/spocc/index.html	Ecology	spocc_occ	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc	1.2.2			(0/1)	(0/1)	(1/1)	(1/1)	True	False
+spolpred			spolpred	A program for predicting the spoligotype from raw sequence reads								To update		Sequence Analysis	spolpred	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/spolpred	1.0.1	spolpred		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+spotyping	1278.0	12.0	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping		SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+sr_bowtie			bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads								To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+sr_bowtie_dataset_annotation			sr_bowtie_dataset_annotation	Maps iteratively small RNA sequencing datasets to reference sequences.								To update	http://artbio.fr	RNA	sr_bowtie_dataset_annotation	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie_dataset_annotation	2.8	bowtie	1.3.1	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+srs_tools			srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata	Compute biodiversity indicators for remote sensing data from Sentinel 2								To update		Ecology		ecology	https://github.com/Marie59/Sentinel_2A/srs_tools	https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools	0.0.1	r-base		(4/7)	(0/7)	(7/7)	(7/7)	True	False
+srst2	205.0	22.0	srst2	Short Read Sequence Typing for Bacterial Pathogens								To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+srst2	205.0	22.0	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2		srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.20	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+sshmm	223.0	5.0	sshmm	ssHMM is an RNA sequence-structure motif finder for RNA-binding protein data, such as CLIP-Seq data								Up-to-date	https://github.molgen.mpg.de/heller/ssHMM	Sequence Analysis, RNA	sshmm	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sshmm	1.0.7	sshmm	1.0.7	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+stacks			stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq	stacks	stacks		Stacks	Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.	Data handling	Mapping, Population genetics	To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis	stacks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks		stacks	2.65	(0/13)	(13/13)	(13/13)	(12/13)	True	False
+stacks2			stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks	Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq								To update	http://catchenlab.life.illinois.edu/stacks/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2	2.55	stacks	2.65	(0/12)	(12/12)	(12/12)	(12/12)	True	False
+star_fusion	1212.0	35.0	star_fusion	STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR								To update		Sequence Analysis, Transcriptomics	star_fusion	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion	https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion	0.5.4-3+galaxy1	star-fusion	1.13.0	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+staramr	12673.0	889.0	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.								Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+stoc			stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic	Tools to analyse STOC data.								To update		Ecology	stoceps	ecology	https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc	https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc	0.0.2			(0/5)	(0/5)	(5/5)	(5/5)	True	False
+stringmlst			stringmlst	Rapid and accurate identification of the sequence type (ST)								To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3	(0/1)	(0/1)	(0/1)	(0/1)	True	True
+structure	2623.0	59.0	structure	for using multi-locus genotype data to investigate population structure.	structure	structure		Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date		Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	(0/1)	(0/1)	(1/1)	(1/1)	True	True
+structureharvester			structureharvester	for parsing STRUCTURE outputs and for performing the Evanno method								Up-to-date		Phylogenetics, Variant Analysis	structureharvester	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structureharvester	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester	0.6.94	structureharvester	0.6.94	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+substitution_rates			subRate1	Estimate substitution rates for non-coding regions								To update		Sequence Analysis, Variant Analysis	substitution_rates	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitution_rates	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitution_rates	1.0.0			(0/1)	(0/1)	(0/1)	(0/1)	True	False
+substitutions			substitutions1	Fetch substitutions from pairwise alignments								To update		Sequence Analysis, Variant Analysis	substitutions	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions	https://github.com/galaxyproject/tools-devteam/tree/main/tools/substitutions	1.0.1	bx-python	0.11.0	(1/1)	(0/1)	(0/1)	(0/1)	True	False
+suite_qiime2__alignment			qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__alignment			qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__alignment			qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__alignment			qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask									To update	https://github.com/qiime2/q2-alignment	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__composition			qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.2.0+q2galaxy.2024.2.1			(4/5)	(4/5)	(4/5)	(2/5)	True	True
+suite_qiime2__composition			qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.2.0+q2galaxy.2024.2.1			(4/5)	(4/5)	(4/5)	(2/5)	True	True
+suite_qiime2__composition			qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.2.0+q2galaxy.2024.2.1			(4/5)	(4/5)	(4/5)	(2/5)	True	True
+suite_qiime2__composition			qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate									To update	https://github.com/qiime2/q2-composition	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition	2024.2.0+q2galaxy.2024.2.1			(4/5)	(4/5)	(4/5)	(2/5)	True	True
+suite_qiime2__cutadapt			qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__cutadapt			qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__cutadapt			qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__cutadapt			qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single									To update	https://github.com/qiime2/q2-cutadapt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__dada2			qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__dada2			qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__dada2			qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__dada2			qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single									To update	http://benjjneb.github.io/dada2/	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__deblur			qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__deblur			qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__deblur			qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__deblur			qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats									To update	https://github.com/biocore/deblur	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__demux			qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.2.0+q2galaxy.2024.2.1			(6/9)	(6/9)	(6/9)	(6/9)	True	True
+suite_qiime2__demux			qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.2.0+q2galaxy.2024.2.1			(6/9)	(6/9)	(6/9)	(6/9)	True	True
+suite_qiime2__demux			qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.2.0+q2galaxy.2024.2.1			(6/9)	(6/9)	(6/9)	(6/9)	True	True
+suite_qiime2__demux			qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts									To update	https://github.com/qiime2/q2-demux	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux	2024.2.0+q2galaxy.2024.2.1			(6/9)	(6/9)	(6/9)	(6/9)	True	True
+suite_qiime2__diversity			qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.2.0+q2galaxy.2024.2.1			(21/22)	(21/22)	(21/22)	(21/22)	True	True
+suite_qiime2__diversity			qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.2.0+q2galaxy.2024.2.1			(21/22)	(21/22)	(21/22)	(21/22)	True	True
+suite_qiime2__diversity			qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.2.0+q2galaxy.2024.2.1			(21/22)	(21/22)	(21/22)	(21/22)	True	True
+suite_qiime2__diversity			qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap									To update	https://github.com/qiime2/q2-diversity	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity	2024.2.0+q2galaxy.2024.2.1			(21/22)	(21/22)	(21/22)	(21/22)	True	True
+suite_qiime2__diversity_lib			qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
+suite_qiime2__diversity_lib			qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
+suite_qiime2__diversity_lib			qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
+suite_qiime2__diversity_lib			qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac									To update	https://github.com/qiime2/q2-diversity-lib	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
+suite_qiime2__emperor			qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__emperor			qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__emperor			qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__emperor			qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot									To update	http://emperor.microbio.me	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
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+suite_qiime2__feature_table			qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.2.2+q2galaxy.2024.2.1			(17/22)	(17/22)	(17/22)	(17/22)	True	True
+suite_qiime2__feature_table			qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.2.2+q2galaxy.2024.2.1			(17/22)	(17/22)	(17/22)	(17/22)	True	True
+suite_qiime2__feature_table			qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.2.2+q2galaxy.2024.2.1			(17/22)	(17/22)	(17/22)	(17/22)	True	True
+suite_qiime2__feature_table			qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose									To update	https://github.com/qiime2/q2-feature-table	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table	2024.2.2+q2galaxy.2024.2.1			(17/22)	(17/22)	(17/22)	(17/22)	True	True
+suite_qiime2__fragment_insertion			qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__fragment_insertion			qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__fragment_insertion			qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__fragment_insertion			qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp									To update	https://github.com/qiime2/q2-fragment-insertion	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion	2024.2.0+q2galaxy.2024.2.1			(3/3)	(3/3)	(3/3)	(3/3)	True	True
+suite_qiime2__longitudinal			qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.2.0+q2galaxy.2024.2.1			(11/11)	(11/11)	(11/11)	(11/11)	True	True
+suite_qiime2__longitudinal			qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.2.0+q2galaxy.2024.2.1			(11/11)	(11/11)	(11/11)	(11/11)	True	True
+suite_qiime2__longitudinal			qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.2.0+q2galaxy.2024.2.1			(11/11)	(11/11)	(11/11)	(11/11)	True	True
+suite_qiime2__longitudinal			qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility									To update	https://github.com/qiime2/q2-longitudinal	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal	2024.2.0+q2galaxy.2024.2.1			(11/11)	(11/11)	(11/11)	(11/11)	True	True
+suite_qiime2__metadata			qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.2.0+q2galaxy.2024.2.1			(3/4)	(3/4)	(3/4)	(3/4)	True	True
+suite_qiime2__metadata			qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.2.0+q2galaxy.2024.2.1			(3/4)	(3/4)	(3/4)	(3/4)	True	True
+suite_qiime2__metadata			qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.2.0+q2galaxy.2024.2.1			(3/4)	(3/4)	(3/4)	(3/4)	True	True
+suite_qiime2__metadata			qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate									To update	https://github.com/qiime2/q2-metadata	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata	2024.2.0+q2galaxy.2024.2.1			(3/4)	(3/4)	(3/4)	(3/4)	True	True
+suite_qiime2__phylogeny			qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
+suite_qiime2__phylogeny			qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
+suite_qiime2__phylogeny			qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
+suite_qiime2__phylogeny			qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds									To update	https://github.com/qiime2/q2-phylogeny	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny	2024.2.0+q2galaxy.2024.2.1			(12/12)	(12/12)	(12/12)	(12/12)	True	True
+suite_qiime2__quality_control			qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.2.0+q2galaxy.2024.2.1			(6/10)	(6/10)	(6/10)	(6/10)	True	True
+suite_qiime2__quality_control			qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.2.0+q2galaxy.2024.2.1			(6/10)	(6/10)	(6/10)	(6/10)	True	True
+suite_qiime2__quality_control			qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.2.0+q2galaxy.2024.2.1			(6/10)	(6/10)	(6/10)	(6/10)	True	True
+suite_qiime2__quality_control			qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads									To update	https://github.com/qiime2/q2-quality-control	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control	2024.2.0+q2galaxy.2024.2.1			(6/10)	(6/10)	(6/10)	(6/10)	True	True
+suite_qiime2__quality_filter			qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.2.0+q2galaxy.2024.2.1			(1/1)	(1/1)	(1/1)	(1/1)	True	True
+suite_qiime2__quality_filter			qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.2.0+q2galaxy.2024.2.1			(1/1)	(1/1)	(1/1)	(1/1)	True	True
+suite_qiime2__quality_filter			qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.2.0+q2galaxy.2024.2.1			(1/1)	(1/1)	(1/1)	(1/1)	True	True
+suite_qiime2__quality_filter			qiime2__quality_filter__q_score									To update	https://github.com/qiime2/q2-quality-filter	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter	2024.2.0+q2galaxy.2024.2.1			(1/1)	(1/1)	(1/1)	(1/1)	True	True
+suite_qiime2__rescript			qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.2.2+q2galaxy.2024.2.1			(0/25)	(0/25)	(0/25)	(0/25)	True	True
+suite_qiime2__rescript			qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.2.2+q2galaxy.2024.2.1			(0/25)	(0/25)	(0/25)	(0/25)	True	True
+suite_qiime2__rescript			qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.2.2+q2galaxy.2024.2.1			(0/25)	(0/25)	(0/25)	(0/25)	True	True
+suite_qiime2__rescript			qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment									To update	https://github.com/nbokulich/RESCRIPt	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript	2024.2.2+q2galaxy.2024.2.1			(0/25)	(0/25)	(0/25)	(0/25)	True	True
+suite_qiime2__sample_classifier			qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.2.0+q2galaxy.2024.2.1			(15/15)	(15/15)	(15/15)	(15/15)	True	True
+suite_qiime2__sample_classifier			qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.2.0+q2galaxy.2024.2.1			(15/15)	(15/15)	(15/15)	(15/15)	True	True
+suite_qiime2__sample_classifier			qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.2.0+q2galaxy.2024.2.1			(15/15)	(15/15)	(15/15)	(15/15)	True	True
+suite_qiime2__sample_classifier			qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize									To update	https://github.com/qiime2/q2-sample-classifier	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier	2024.2.0+q2galaxy.2024.2.1			(15/15)	(15/15)	(15/15)	(15/15)	True	True
+suite_qiime2__taxa			qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__taxa			qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__taxa			qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__taxa			qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table									To update	https://github.com/qiime2/q2-taxa	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa	2024.2.0+q2galaxy.2024.2.1			(4/4)	(4/4)	(4/4)	(4/4)	True	True
+suite_qiime2__vsearch			qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.2.0+q2galaxy.2024.2.1			(8/8)	(8/8)	(8/8)	(7/8)	True	True
+suite_qiime2__vsearch			qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.2.0+q2galaxy.2024.2.1			(8/8)	(8/8)	(8/8)	(7/8)	True	True
+suite_qiime2__vsearch			qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.2.0+q2galaxy.2024.2.1			(8/8)	(8/8)	(8/8)	(7/8)	True	True
+suite_qiime2__vsearch			qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref									To update	https://github.com/qiime2/q2-vsearch	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch	2024.2.0+q2galaxy.2024.2.1			(8/8)	(8/8)	(8/8)	(7/8)	True	True
+suite_qiime2_core												To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core				(0/1)	(0/1)	(0/1)	(0/1)	True	True
+suite_qiime2_core												To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core				(0/1)	(0/1)	(0/1)	(0/1)	True	True
+suite_qiime2_core												To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core				(0/1)	(0/1)	(0/1)	(0/1)	True	True
+suite_qiime2_core												To update		Statistics, Metagenomics, Sequence Analysis		q2d2		https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core				(0/1)	(0/1)	(0/1)	(0/1)	True	True
+suite_qiime2_core__tools			qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.2.1+dist.he188c3c2			(2/3)	(2/3)	(2/3)	(2/3)	True	True
+suite_qiime2_core__tools			qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.2.1+dist.he188c3c2			(2/3)	(2/3)	(2/3)	(2/3)	True	True
+suite_qiime2_core__tools			qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.2.1+dist.he188c3c2			(2/3)	(2/3)	(2/3)	(2/3)	True	True
+suite_qiime2_core__tools			qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq									To update	https://qiime2.org	Metagenomics, Sequence Analysis, Statistics		q2d2	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools	2024.2.1+dist.he188c3c2			(2/3)	(2/3)	(2/3)	(2/3)	True	True
+suite_snvphyl				SNVPhyl suite defining all dependencies for SNVPhyl								To update		Sequence Analysis	suite_snvphyl_1_2_3	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/suite_snvphyl				(0/1)	(0/1)	(0/1)	(0/1)	True	False
+syndiva	30.0	2.0	syndiva	SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.								To update		Proteomics	syndiva	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/SynDivA	https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva	1.0	clustalo	1.2.4	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+t2ps	457.0	31.0	Draw_phylogram	Draw phylogeny								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+t2t_report	947.0	26.0	t2t_report	Summarize taxonomy								To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+t_coffee	8690.0	70.0	t_coffee	T-Coffee								To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+tapscan			tapscan_classify	Search for transcription associated proteins (TAPs)								To update	https://plantcode.cup.uni-freiburg.de/tapscan/	Proteomics	tapscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	https://github.com/bgruening/galaxytools/tree/master/tools/tapscan	4.76+galaxy0	hmmer	3.4	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+tarfast5			tarfast5	produces a tar.gz archive of fast5 sequence files								To update	http://artbio.fr	Nanopore	tarfast5	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/tarfast5	https://github.com/ARTbio/tools-artbio/tree/main/tools/tarfast5	0.6.1	pigz		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+targetfinder	713.0	37.0	targetfinder	Plant small RNA target prediction tool								Up-to-date	https://github.com/carringtonlab/TargetFinder.git	RNA	targetfinder	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder/	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/targetfinder	1.7	targetfinder	1.7	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+tasmanian_mismatch			tasmanian_mismatch	Analysis of positional mismatches								Up-to-date		Sequence Analysis	tasmanian_mismatch	iuc	https://github.com/nebiolabs/tasmanian-mismatch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch	1.0.7	tasmanian-mismatch	1.0.7	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+taxonomy_filter_refseq			taxonomy_filter_refseq	Filter RefSeq by taxonomy								To update	https://github.com/pvanheus/ncbitaxonomy	Sequence Analysis, Genome annotation	taxonomy_filter_refseq	iuc	https://github.com/galaxyproject/tools-iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq	0.3.0	rust-ncbitaxonomy	1.0.7	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+taxonomy_krona_chart	27426.0	1801.0	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona		Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+tb-profiler			tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler		tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	4.4.1	tb-profiler	6.2.0	(1/1)	(1/1)	(1/1)	(0/1)	True	True
+tbl2gff3	1584.0	229.0	tbl2gff3	Table to GFF3								To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	Convert Formats, Sequence Analysis	tbl2gff3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3	1.2	bcbiogff	0.6.6	(0/1)	(1/1)	(1/1)	(1/1)	True	False
+te_finder	81.0	7.0	te_finder	Transposable element insertions finder	tefinder	tefinder		TEfinder	A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data.	Genome indexing, Variant calling, PCR primer design	Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation	To update	https://github.com/VistaSohrab/TEfinder	Sequence Analysis	te_finder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/te_finder/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder	1.0.1	samtools	1.20	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+telescope			telescope_assign	Single locus resolution of Transposable ELEment expression.	Telescope-expression	Telescope-expression		Telescope	Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope.	Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping	RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly	Up-to-date	https://github.com/mlbendall/telescope/	Genome annotation	telescope_assign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/telescope	https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope	1.0.3	telescope	1.0.3	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+tetoolkit			tetoolkit_tetranscripts	The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases.								Up-to-date	http://hammelllab.labsites.cshl.edu/software/	Sequence Analysis	tetoolkit	iuc	https://github.com/mhammell-laboratory/TEtranscripts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit	2.2.3	tetranscripts	2.2.3	(0/1)	(1/1)	(1/1)	(0/1)	True	False
+tetyper	69.0	8.0	tetyper	Type a specific transposable element (TE) of interest from paired-end sequencing data.								Up-to-date	https://github.com/aesheppard/TETyper	Sequence Analysis	tetyper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper	1.1	tetyper	1.1	(1/1)	(0/1)	(1/1)	(0/1)	True	False
+tgsgapcloser	460.0	36.0	tgsgapcloser	TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly.	TGS-GapCloser	TGS-GapCloser		TGS-GapCloser	TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads.	Genome assembly, Read mapping, Scaffolding, Localised reassembly	Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping	To update	https://github.com/BGI-Qingdao/TGS-GapCloser	Assembly	tgsgapcloser	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser	1.0.3	tgsgapcloser	1.2.1	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+tn93	113.0	7.0	tn93_readreduce, tn93, tn93_cluster, tn93_filter	Compute distances between sequences								To update	https://github.com/veg/tn93/	Sequence Analysis	tn93	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93	1.0.6	tn93	1.0.14	(4/4)	(0/4)	(4/4)	(0/4)	True	False
+tooldistillator			tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator		ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.8.4.1	tooldistillator	0.8.4.1	(0/2)	(0/2)	(2/2)	(2/2)	True	True
+tophat	1.0		tophat	Tophat for Illumina								To update		RNA, Next Gen Mappers	tophat	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat	1.5.0	samtools	1.20	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+tophat2	24167.0	312.0	tophat2	Tophat - fast splice junction mapper for RNA-Seq reads								To update	http://ccb.jhu.edu/software/tophat/index.shtml	RNA, Next Gen Mappers	tophat2	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2	https://github.com/galaxyproject/tools-devteam/tree/main/tools/tophat2	2.1.1	bowtie2	2.5.3	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+transdecoder	5468.0	348.0	transdecoder	TransDecoder finds coding regions within transcripts	TransDecoder	TransDecoder		TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.	Coding region prediction, de Novo sequencing, De-novo assembly	Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing	To update	https://transdecoder.github.io/	Transcriptomics, RNA	transdecoder	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transdecoder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder	5.5.0	transdecoder	5.7.1	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+transit			gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit		TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	(5/5)	(5/5)	(5/5)	(0/5)	True	True
+translate_bed	643.0	49.0	translate_bed	Translate BED transcript CDS or cDNA in 3 frames								To update	http://rest.ensembl.org/	Proteomics	translate_bed	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed	0.1.0			(1/1)	(1/1)	(1/1)	(0/1)	True	False
+translate_bed_sequences	57.0	6.0	translate_bed_sequences	Perform 3 frame translation of BED file augmented with a sequence column								To update		Proteomics	translate_bed_sequences	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences	0.2.0	biopython	1.70	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+transtermhp	229.0	5.0	transtermhp	Finds rho-independent transcription terminators in bacterial genomes	transtermhp	transtermhp		TransTermHP	TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	To update	https://transterm.cbcb.umd.edu	Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp		transtermhp	2.09	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+trim_galore	238699.0	2334.0	trim_galore	Trim Galore adaptive quality and adapter trimmer	trim_galore	trim_galore		Trim Galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/	Sequence Analysis, Fastq Manipulation	trim_galore	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore	0.6.7	trim-galore	0.6.10	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+trinity	12733.0	678.0	trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats	Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq	trinity	trinity		Trinity	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.	Transcriptome assembly	Transcriptomics, Gene expression, Gene transcripts	Up-to-date	https://github.com/trinityrnaseq/trinityrnaseq	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity	2.15.1	trinity	2.15.1	(9/13)	(13/13)	(13/13)	(13/13)	True	False
+trinotate	1796.0	151.0	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	trinotate	trinotate		Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.	Gene functional annotation	Gene expression, Transcriptomics	To update	https://trinotate.github.io/	Transcriptomics, RNA	trinotate	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate	3.2.2	trinotate	4.0.2	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+trna_prediction	2935.0	236.0	aragorn_trna, trnascan	Aragorn predicts tRNA and tmRNA in nucleotide sequences.								To update	http://mbioserv2.mbioekol.lu.se/ARAGORN/	RNA	trna_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/trna_prediction	0.6	aragorn	1.2.41	(0/2)	(2/2)	(2/2)	(0/2)	True	False
+trycycler			trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample	Trycycler toolkit wrappers								Up-to-date	https://github.com/rrwick/Trycycler	Assembly	trycycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler	0.5.5	trycycler	0.5.5	(0/5)	(5/5)	(5/5)	(5/5)	True	True
+tsebra	5.0		tsebra	This tool has been developed to combine BRAKER predictions.	tsebra	tsebra		TSEBRA	TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies.	Homology-based gene prediction, Alternative splicing prediction	Gene expression, RNA-Seq, Gene transcripts, Model organisms	Up-to-date	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra	1.1.2.4	tsebra	1.1.2.4	(0/1)	(0/1)	(1/1)	(1/1)	True	False
+ucsc_blat			ucsc_blat	Standalone blat sequence search command line tool	blat	blat		BLAT	Fast, accurate spliced alignment of DNA sequences.	Sequence alignment	Sequence analysis	To update	http://genome.ucsc.edu/goldenPath/help/blatSpec.html	Sequence Analysis	ucsc_blat	yating-l		https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat	377	ucsc-blat	445	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+ucsc_custom_track	393.0	45.0	build_ucsc_custom_track_1	Build custom track for UCSC genome browser								To update		Sequence Analysis	ucsc_custom_track	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	https://github.com/galaxyproject/tools-devteam/tree/main/tools/ucsc_custom_track	1.0.1	python		(1/1)	(0/1)	(1/1)	(0/1)	True	False
+umi_tools			umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist	UMI-tools extract - Extract UMIs from fastq	umi-tools	umi-tools		UMI-tools	Tools for handling Unique Molecular Identifiers in NGS data sets.	Sequencing quality control	NGS, Sequence sites, features and motifs, Quality affairs	To update	https://github.com/CGATOxford/UMI-tools	Sequence Analysis, Transcriptomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools	1.1.2	umi_tools	1.1.5	(5/5)	(5/5)	(5/5)	(5/5)	True	False
+unicycler	65732.0	1558.0	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler		Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.0	unicycler	0.5.0	(1/1)	(1/1)	(1/1)	(1/1)	True	True
+unipept	5005.0	115.0	unipept	Unipept retrieves metaproteomics information	unipept	unipept		Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		(1/1)	(1/1)	(1/1)	(0/1)	True	True
+uniprot_rest_interface	2406.0	132.0	uniprot	UniProt ID mapping and sequence retrieval								To update	https://github.com/jdrudolph/uniprot	Proteomics, Sequence Analysis	uniprot_rest_interface	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface	0.4	requests		(1/1)	(1/1)	(1/1)	(0/1)	True	False
+uniprotxml_downloader	1360.0	79.0	uniprotxml_downloader	Download UniProt proteome in XML or fasta format								To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests		(0/1)	(1/1)	(1/1)	(0/1)	True	True
+usher	1060.0	5.0	usher_matutils, usher	UShER toolkit wrappers	usher	usher		usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	(0/2)	(0/2)	(2/2)	(0/2)	True	True
+valet	637.0	20.0	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet		VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	(1/1)	(0/1)	(1/1)	(1/1)	True	True
+validate_fasta_database	86.0	25.0	validate_fasta_database	runs Compomics database identification tool on any FASTA database, and separates valid and invalid entries based on a series of checks.								To update		Fasta Manipulation, Proteomics	validate_fasta_database	galaxyp		https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/validate_fasta_database	0.1.5	validate-fasta-database	1.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+vapor	3164.0	94.0	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor		VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	(1/1)	(0/1)	(1/1)	(0/1)	True	True
+varvamp			varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp		varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology	Up-to-date	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	True
+vcf2snvalignment			vcf2snvalignment	Generates multiple alignment of variant calls								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	vcf2snvalignment	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/vcf2snvalignment	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+vegan			vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan		vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	(3/3)	(0/3)	(3/3)	(0/3)	True	True
+velvet	12218.0	1280.0	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet		Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	(2/2)	(2/2)	(2/2)	(2/2)	True	True
+velvet_optimiser			velvetoptimiser	Automatically optimize Velvet assemblies	velvetoptimiser	velvetoptimiser		VelvetOptimiser	This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly.	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	To update		Assembly	velvetoptimiser	simon-gladman	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser	2.2.6+galaxy2	velvet	1.2.10	(1/1)	(1/1)	(1/1)	(0/1)	True	True
+venn_list	5067.0	248.0	venn_list	Draw Venn Diagram (PDF) from lists, FASTA files, etc								To update	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	Graphics, Sequence Analysis, Visualization	venn_list	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list	0.1.2	galaxy_sequence_utils	1.1.5	(1/1)	(0/1)	(1/1)	(1/1)	True	False
+verify_map			verify_map	Checks the mapping quality of all BAM(s)								Up-to-date	https://snvphyl.readthedocs.io/en/latest/	Sequence Analysis	verify_map	nml	https://github.com/phac-nml/snvphyl-galaxy	https://github.com/phac-nml/snvphyl-galaxy/tree/development/tools/snvphyl-tools/verify_map	1.8.2	snvphyl-tools	1.8.2	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+verkko	22.0	9.0	verkko	Telomere-to-telomere assembly pipeline								To update	https://github.com/marbl/verkko	Assembly	verkko	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko	https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko	1.3.1	verkko	2.0	(0/1)	(0/1)	(1/1)	(0/1)	True	False
+vg			vg_convert, vg_deconstruct, vg_view	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods								To update	https://github.com/vgteam/vg	Sequence Analysis, Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg	1.23.0	vg	1.56.0	(0/3)	(0/3)	(3/3)	(3/3)	True	False
+vienna_rna	799.0		viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup	ViennaRNA - Prediction and comparison of RNA secondary structures								To update	http://www.tbi.univie.ac.at/RNA/	RNA	viennarna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna	2.2.10	viennarna	2.6.4	(0/23)	(0/23)	(21/23)	(0/23)	True	False
+vigiechiro			vigiechiro_bilanenrichipf, vigiechiro_bilanenrichirp, vigiechiro_idcorrect_2ndlayer, vigiechiro_idvalid	Tools created by the vigiechiro team to analyses and identify chiro sounds files.								To update	https://www.vigienature-ecole.fr/les-observatoires/le-protocole-vigie-chiro	Ecology	vigiechiro	ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	https://github.com/galaxyecology/tools-ecology/tree/master/tools/vigiechiro	0.1.1			(0/4)	(0/4)	(4/4)	(4/4)	True	False
+virAnnot			virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers								To update	https://github.com/marieBvr/virAnnot	Metagenomics	virannot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot	1.0.0+galaxy0	biopython	1.70	(0/3)	(0/3)	(3/3)	(3/3)	True	True
+volcanoplot	30946.0	1749.0	volcanoplot	Tool to create a Volcano Plot								To update		Visualization, Transcriptomics, Statistics	volcanoplot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot	0.0.5	r-ggplot2	2.2.1	(1/1)	(1/1)	(1/1)	(1/1)	True	False
+vsearch	8507.0	182.0	vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting	VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences.	vsearch	vsearch		VSEARCH	High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	To update	https://github.com/torognes/vsearch	Sequence Analysis	vsearch	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch	2.8.3	vsearch	2.28.1	(8/8)	(8/8)	(8/8)	(8/8)	True	True
+vsnp			vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics	The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees.								To update	https://github.com/USDA-VS/vSNP	Sequence Analysis	vsnp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp	3.0.6	pysam	0.22.1	(0/5)	(0/5)	(0/5)	(0/5)	True	False
+vt			vt_@BINARY@, vt_@BINARY@	A tool set for short variant discovery in genetic sequence data.								To update		Sequence Analysis, Variant Analysis	vt	bgruening	https://github.com/atks/vt	https://github.com/bgruening/galaxytools/tree/master/tools/vt	0.2	vt	2015.11.10	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+wade			wade	identify regions of interest								To update	https://github.com/phac-nml/wade	Sequence Analysis	wade	nml	https://github.com/phac-nml/wade	https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade	0.2.5+galaxy1	wade	0.2.6	(0/1)	(0/1)	(0/1)	(0/1)	True	False
+weather_app			simple_weather	provides simple weather in text format								To update	http://wttr.in/	Visualization, Web Services	simpleweather	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app	https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app	0.1.2	curl		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+weightedaverage			wtavg	Assign weighted-average of the values of features overlapping an interval								To update		Sequence Analysis, Variant Analysis	weightedaverage	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage	https://github.com/galaxyproject/tools-devteam/tree/main/tools/weightedaverage	1.0.1	galaxy-ops	1.1.0	(1/1)	(0/1)	(0/1)	(0/1)	True	False
+windowmasker	85.0		windowmasker_mkcounts, windowmasker_ustat	Identify repetitive regions using WindowMasker								To update	https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/	Sequence Analysis	windowmasker	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker	1.0	blast	2.15.0	(0/2)	(2/2)	(2/2)	(0/2)	True	False
+windowsplitter			winSplitter	Make windows								To update		Sequence Analysis, Variant Analysis	windowsplitter	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter	https://github.com/galaxyproject/tools-devteam/tree/main/tools/windowsplitter	1.0.1	bx-python	0.11.0	(1/1)	(0/1)	(0/1)	(0/1)	True	False
+wtdbg	1660.0	116.0	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2		wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	(0/1)	(0/1)	(1/1)	(1/1)	True	True
+xarray			timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select	xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory.								To update	http://xarray.pydata.org	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/	https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray	2022.3.0	xarray		(5/6)	(2/6)	(6/6)	(5/6)	True	False
+xpore			xpore_dataprep, xpore_diffmod	Identification and quantification of differential RNA modifications from direct RNA sequencing								To update	https://github.com/GoekeLab/xpore	Nanopore	xpore	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/xpore	https://github.com/ARTbio/tools-artbio/tree/main/tools/xpore	2.1+galaxy0	xpore	2.1	(0/2)	(0/2)	(0/2)	(0/2)	True	False
+yac_clipper			yac	Clips 3' adapters for small RNA sequencing reads.								To update	http://artbio.fr	RNA, Fastq Manipulation	yac_clipper	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper	https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper	2.5.1	python		(0/1)	(0/1)	(0/1)	(0/1)	True	False
+yahs	344.0	64.0	yahs	Yet Another Hi-C scaffolding tool								Up-to-date	https://github.com/c-zhou/yahs	Assembly	yahs	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs	https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs	1.2a.2	yahs	1.2a.2	(1/1)	(1/1)	(1/1)	(0/1)	True	False
+zoo_project_ogc_api_processes			zoo_project_ogc_api_processes	This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.								To update	https://github.com/AquaINFRA/galaxy	Ecology		ecology	https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper	https://github.com/galaxyecology/tools-ecology/tree/master/tools/zoo_project_ogc_api_processes	0.1.0	r-base		(0/1)	(0/1)	(1/1)	(0/1)	True	False