diff --git a/results/all_tools.tsv b/results/all_tools.tsv
index 1e6d2a88..13716eae 100644
--- a/results/all_tools.tsv
+++ b/results/all_tools.tsv
@@ -86,6 +86,7 @@ wade			wade	identify regions of interest						To update	https://github.com/phac-
 camera			abims_CAMERA_annotateDiffreport, abims_CAMERA_combinexsAnnos							To update		Metabolomics	camera	workflow4metabolomics		1.48.0	r-snow	0.4_1	(1/2)	(2/2)	(2/2)
 correlation_analysis			correlation_analysis	[Metabolomics][W4M] Metabolites Correlation Analysis						To update	http://workflow4metabolomics.org	Metabolomics	correlation_analysis	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/correlation_analysis/	1.0.1+galaxy0	r-batch	1.1_4	(0/1)	(0/1)	(0/1)
 genform	68.0		genform	genform: generation of molecular formulas by high-resolution MS and MS/MS data						To update	https://sourceforge.net/projects/genform/	Metabolomics	genform	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/		genform	r8	(0/1)	(0/1)	(1/1)
+influx_data_manager			influx_data_manager	Handling influx_si data inputs in Galaxy workflows						Up-to-date	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/	Metabolomics	influx_si_data_manager	workflow4metabolomics	https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager	1.0.0	influx-si-data-manager	1.0.0	(0/1)	(0/1)	(0/1)
 influx_si			influx_si	metabolic flux estimation based on [in]stationary labeling						Up-to-date	https://github.com/sgsokol/influx	Metabolomics	influx_si	workflow4metabolomics	https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/influx_si/	7.0.1	influx_si	7.0.1	(0/1)	(0/1)	(0/1)
 ipo			ipo4retgroup, ipo4xcmsSet	[W4M][LC-MS] IPO						To update	https://github.com/rietho/IPO	Metabolomics	ipo	lecorguille	https://github.com/rietho/IPO	1.10.0	bioconductor-ipo	1.28.0	(0/2)	(0/2)	(0/2)
 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	1.3.0+galaxy1	isoplot	1.3.1	(0/1)	(0/1)	(1/1)
@@ -147,7 +148,7 @@ segmetrics	3.0	2.0	ip_segmetrics	Image segmentation and object detection perform
 slice_image	102.0		ip_slice_image	Slice image	galaxy_image_analysis	Galaxy Image Analysis	Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	slice_image	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/	0.3-2	scikit-image		(0/1)	(0/1)	(1/1)
 split_labelmap	42.0		ip_split_labelmap	Split Labelmaps	galaxy_image_analysis	Galaxy Image Analysis	Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/bmcv	Imaging	split_labelmap	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_labelmaps/	0.2-2	scikit-image		(0/1)	(0/1)	(1/1)
 spot_detection_2d	16.0	3.0	ip_spot_detection_2d	Spot detection in 2D image sequence	galaxy_image_analysis	Galaxy Image Analysis	Developed within the Biomedical Computer Vision (BMCV) Group Heidelberg.	Image analysis	Imaging, Bioinformatics	To update	https://github.com/BMCV/galaxy-image-analysis	Imaging	spot_detection_2d	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/	0.0.3-2	imageio		(0/1)	(0/1)	(1/1)
-superdsm	16.0	2.0	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		Up-to-date	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	0.1.3	superdsm	0.1.3	(0/1)	(0/1)	(1/1)
+superdsm	16.0	2.0	ip_superdsm	Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images	superdsm	SuperDSM	SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.	Image analysis		To update	https://github.com/bmcv	Imaging	superdsm	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/superdsm/	0.1.3	superdsm	0.2.0	(0/1)	(0/1)	(1/1)
 unzip	5370.0	508.0	unzip	Unzip file						To update	https://github.com/bmcv	Convert Formats	unzip	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/unzip/	6.0	unzip		(0/1)	(1/1)	(1/1)
 visceral-evaluatesegmentation			ip_visceral_evaluatesegmentation	Visceral Project - Evaluate Segmentation Tool						To update	https://github.com/bmcv	Imaging	visceral_evaluatesegmentation	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/visceral-evaluatesegmentation	0.5-2	visceral-evaluatesegmentation	2015.07.03	(0/1)	(0/1)	(1/1)
 wsi_extract_top_view	38.0		ip_wsi_extract_top_view	WSI Extract Top View						To update	https://github.com/bmcv	Imaging	wsi_extract_top_view	imgteam	https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/	0.2-2	scikit-image		(0/1)	(0/1)	(1/1)
@@ -272,13 +273,13 @@ tables_arithmetic_operations	2207.0	14.0	tables_arithmetic_operations	Arithmetic
 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	1.0.0			(1/1)	(0/1)	(1/1)
 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	1.0.0	R		(1/1)	(0/1)	(1/1)
 snpfreq	37.0	7.0	hgv_snpFreq	snpFreq significant SNPs in case-control data						To update		Variant Analysis, Statistics	snpfreq	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/hgv/snpfreq	1.0.1	R		(1/1)	(1/1)	(1/1)
-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	1.0.0	taxonomy	0.9.0	(0/1)	(0/1)	(1/1)
-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	1.1.1	taxonomy	0.9.0	(0/1)	(0/1)	(1/1)
+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	1.0.0	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)
+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	1.1.1	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)
 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/	1.2+galaxy0	gawk		(1/1)	(1/1)	(1/1)
-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	1.0.1	taxonomy	0.9.0	(0/1)	(0/1)	(1/1)
-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	1.0.0	taxonomy	0.9.0	(0/1)	(1/1)	(1/1)
-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	1.0.0	taxonomy	0.9.0	(0/1)	(0/1)	(1/1)
-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	1.0.0	taxonomy	0.9.0	(0/1)	(0/1)	(1/1)
+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	1.0.1	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)
+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	1.0.0	taxonomy	0.10.0	(0/1)	(1/1)	(1/1)
+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	1.0.0	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)
+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	1.0.0	taxonomy	0.10.0	(0/1)	(0/1)	(1/1)
 vcftools_annotate	171.0	24.0	vcftools_annotate	Annotate VCF using custom/user-defined annotations						To update	https://vcftools.github.io/	Variant Analysis	vcftools_annotate	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_annotate	0.1	echo		(1/1)	(0/1)	(1/1)
 vcftools_compare	531.0	34.0	vcftools_compare	Compare VCF files to get overlap and uniqueness statistics						To update	https://vcftools.github.io/	Variant Analysis	vcftools_compare	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_compare	0.1	tabix	1.11	(0/1)	(0/1)	(1/1)
 vcftools_consensus			vcftools_consensus	Apply VCF variants to a fasta file to create consensus sequence						To update	https://vcftools.github.io/	Variant Analysis	vcftools_consensus	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_consensus	0.1.11	samtools	1.19.2	(0/1)	(0/1)	(0/1)
@@ -338,7 +339,7 @@ graph_converter			graph_converter	Convert between different graph formats						T
 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	0.1	GraphClust		(0/1)	(0/1)	(0/1)
 graphmap			graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.						To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.3	(0/2)	(0/2)	(2/2)
 hclust2			hclust2	Plots heatmaps						To update	https://bitbucket.org/nsegata/hclust2/	Data Visualization	hclust2	rnateam	https://github.com/yuanbit/galaxytools/tree/hclust2/tools/hclust2	0.99	hclust2	1.0.0	(0/1)	(0/1)	(0/1)
-hictk			hictk	hictk, a blazing-fast toolkit to work with .hic and .cool files						Up-to-date	https://github.com/paulsengroup/hictk		hictk	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	0.0.8	hictk	0.0.8	(0/1)	(0/1)	(0/1)
+hictk			hictk	hictk, a blazing-fast toolkit to work with .hic and .cool files						Up-to-date	https://github.com/paulsengroup/hictk		hictk	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hictk	0.0.8	hictk	0.0.8	(0/1)	(0/1)	(1/1)
 hicup			hicup2juicer, hicup_deduplicator, hicup_digester, hicup_filter, hicup_hicup, hicup_mapper, hicup_truncater	The HiCUP-Pipeline from the Bioinformatics Babraham Institute.						To update	https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html	Epigenetics	hicup	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hicup	0.9.2			(7/7)	(0/7)	(7/7)
 hifiasm	1410.0	297.0	hifiasm	A fast haplotype-resolved de novo assembler						Up-to-date	https://github.com/chhylp123/hifiasm	Assembly	hifiasm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/hifiasm	0.19.8	hifiasm	0.19.8	(1/1)	(1/1)	(1/1)
 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				(0/1)	(0/1)	(0/1)
@@ -493,9 +494,9 @@ aldex2	129.0	13.0	aldex2	Performs analysis Of differential abundance taking samp
 allegro			allegro	Linkage and haplotype analysis from deCODE	allegro	Allegro	It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome.	Sequence motif discovery	Sequence analysis, Transcription factors and regulatory sites, DNA	To update	http://www.decode.com/software/	Variant Analysis	allegro	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/allegro/	@VER@.0	allegro	3	(0/1)	(0/1)	(0/1)
 amplican	53.0	12.0	amplican	AmpliCan is an analysis tool for genome editing.	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	1.14.0	bioconductor-amplican	1.24.0	(0/1)	(0/1)	(1/1)
 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	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	2.7.22			(0/19)	(0/19)	(19/19)
-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 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	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	3.11.26	ncbi-amrfinderplus	3.11.26	(0/1)	(0/1)	(1/1)
+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 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	3.11.26	ncbi-amrfinderplus	3.12.8	(0/1)	(0/1)	(1/1)
 ancombc	7.0	4.0	ancombc	Performs analysis of compositions of microbiomes with bias correction.	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	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	(0/1)	(0/1)	(1/1)
-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/	0.10.3	anndata	0.6.22.post1	(5/5)	(3/5)	(5/5)
+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/	0.10.3	anndata	0.6.22.post1	(5/5)	(4/5)	(5/5)
 annotatemyids	26115.0	1175.0	annotatemyids	annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages	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		To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	Genome annotation	annotatemyids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids	3.17.0	bioconductor-org.hs.eg.db	3.18.0	(1/1)	(1/1)	(1/1)
 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	2.4.0	arriba	2.4.0	(0/3)	(3/3)	(3/3)
 art			art_454, art_illumina, art_solid	Simulator for Illumina, 454, and SOLiD sequencing data	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	2014.11.03.0	art	2016.06.05	(0/3)	(0/3)	(0/3)
@@ -503,7 +504,7 @@ artic			artic_guppyplex, artic_minion	The artic pipeline is designed to help run
 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	17.02	rjchallis-assembly-stats	17.02	(0/1)	(0/1)	(0/1)
 augustus	8864.0	516.0	augustus, augustus_training	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.	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	3.4.0	augustus	3.5.0	(2/2)	(2/2)	(2/2)
 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	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		3.0.5+galaxy0	b2btools	3.0.6	(0/1)	(0/1)	(1/1)
-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	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	1.8.2	bakta	1.9.2	(0/1)	(1/1)	(1/1)
+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	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	1.9.2	bakta	1.9.2	(0/1)	(1/1)	(1/1)
 bam_to_scidx	128.0	4.0	bam_to_scidx	Contains a tool that converts a BAM file to an ScIdx file.						To update	https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx	Convert Formats	bam_to_scidx	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bam_to_scidx	1.0.1	openjdk		(1/1)	(0/1)	(1/1)
 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		bamutil	1.0.15	(1/2)	(1/2)	(1/2)
 bandage	44390.0	2016.0	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	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	2022.09	bandage_ng	2022.09	(2/2)	(2/2)	(2/2)
@@ -513,7 +514,7 @@ barrnap	3938.0	160.0	barrnap	Contains the Barrnap tool for finding ribosomal RNA
 basil	266.0	35.0	basil	Breakpoint detection, including large insertions						Up-to-date	https://github.com/seqan/anise_basil	Variant Analysis	basil	iuc		1.2.0	anise_basil	1.2.0	(1/1)	(0/1)	(1/1)
 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	0.0.11	bax2bam	0.0.11	(1/1)	(0/1)	(1/1)
 bayescan	64.0	8.0	BayeScan	Detecting natural selection from population-based genetic data	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/	2.1	bayescan	2.0.1	(0/1)	(0/1)	(1/1)
-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.						To update	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	39.01	bbmap	39.06	(1/6)	(1/6)	(5/6)
+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	39.06	bbmap	39.06	(6/6)	(1/6)	(5/6)
 bcftools	524.0	78.0	bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@	BCFtools toolkit wrappers	bcftools	BCFtools	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.	Data handling, Variant calling	Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment	To update	https://samtools.github.io/bcftools/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools	1.15.1	bcftools	1.19	(0/5)	(0/5)	(0/5)
 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	0.2.2	bctools	0.2.2	(0/7)	(0/7)	(7/7)
 beacon2			beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff	beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI).	GA4GH Beacon					Up-to-date	https://github.com/EGA-archive/beacon2-ri-tools/tree/main	Variant Analysis	beacon2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2	2.0.0	beacon2-ri-tools	2.0.0	(0/3)	(0/3)	(3/3)
@@ -525,18 +526,19 @@ berokka			berokka	Berokka is used to trim, circularise, orient & filter long rea
 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	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	1.4.3	binning_refiner	1.4.3	(0/1)	(0/1)	(1/1)
 bioext			bioext_bam2msa, bioext_bealign	A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more!						To update	https://pypi.python.org/pypi/biopython-extensions/	Next Gen Mappers		iuc	https://github.com/davebx/bioext-gx/	0.20.4	python-bioext	0.21.2	(2/2)	(0/2)	(2/2)
 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	0.1.0	python		(1/1)	(0/1)	(1/1)
-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.						To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	2.1.15	biom-format	2.1.7	(2/6)	(2/6)	(1/6)
+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	"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	2.1.15	biom-format	2.1.7	(2/6)	(2/6)	(1/6)
 bioperl			bp_genbank2gff3	Converts GenBank format files to GFF3	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	1.1	perl-bioperl	1.7.8	(1/1)	(1/1)	(1/1)
 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	2.3.3	biscot	2.3.3	(0/1)	(0/1)	(1/1)
 blast			magicblast	Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome						Up-to-date	https://ncbi.github.io/magicblast/	Next Gen Mappers	magicblast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/blast	1.7.0	magicblast	1.7.0	(0/1)	(0/1)	(1/1)
 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	1.1	bcbiogff	0.6.6	(1/1)	(1/1)	(1/1)
 bowtie2	380252.0	5136.0	bowtie2	Bowtie2: Fast and sensitive read alignment	bowtie2	Bowtie 2	Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.	Read mapping	Mapping, Genomics, Mapping	To update	http://bowtie-bio.sourceforge.net/bowtie2	Next Gen Mappers	bowtie2	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2	2.5.0	bowtie2	2.5.3	(1/1)	(1/1)	(1/1)
 bracken	18351.0	326.0	est_abundance	Bayesian Reestimation of Abundance with KrakEN	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	2.9	bracken	2.9	(0/1)	(0/1)	(1/1)
-breseq	1871.0	50.0	breseq	Predicts mutations in microbial genomes	breseq	breseq	Runs Breseq software on a set of fastq files.	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	To update	https://github.com/barricklab/breseq	Variant Analysis	breseq	iuc		0.35.5	breseq	0.38.2	(0/1)	(1/1)	(1/1)
+breseq	1871.0	50.0	breseq	Predicts mutations in microbial genomes	breseq	breseq	Runs Breseq software on a set of fastq files.	Polymorphism detection	Sequencing, Sequence analysis, DNA mutation	To update	https://github.com/barricklab/breseq	Variant Analysis	breseq	iuc		0.35.5	breseq	0.38.3	(0/1)	(1/1)	(1/1)
 busco	86180.0	1804.0	busco	BUSCO assess genome and annotation completeness	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/	5.5.0	busco	5.6.1	(1/1)	(1/1)	(1/1)
 bwa	957912.0	5279.0	bwa_mem, bwa	Wrapper for bwa mem, aln, sampe, and samse	bwa	BWA	Fast, accurate, memory-efficient aligner for short and long sequencing reads	Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment	Mapping	Up-to-date	http://bio-bwa.sourceforge.net/	Next Gen Mappers	bwa	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa	0.7.17	bwa	0.7.17	(2/2)	(2/2)	(2/2)
 bwa_mem2	44386.0	1220.0	bwa_mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa.	bwa-mem2	Bwa-mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case,  dataset and the running machine.	Sequence alignment	Mapping	Up-to-date	https://github.com/bwa-mem2/bwa-mem2	Next Gen Mappers	bwa_mem2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa_mem2	2.2.1	bwa-mem2	2.2.1	(1/1)	(1/1)	(1/1)
 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	0.2.6	bwameth	0.2.7	(1/1)	(1/1)	(1/1)
+cactus			cactus_cactus, cactus_export	Cactus is a reference-free whole-genome multiple alignment program	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	2.7.1			(0/2)	(2/2)	(2/2)
 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	1.0.0	numpy		(0/1)	(0/1)	(0/1)
 calculate_numeric_param	1393.0	8.0	calculate_numeric_param	Calculate a numeric parameter value using integer and float values.						To update		Text Manipulation	calculate_numeric_param	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_numeric_param	0.1.0			(0/1)	(0/1)	(1/1)
 cat			cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise	Contig Annotation Tool (CAT)						To update	https://github.com/dutilh/CAT	Metagenomics	contig_annotation_tool	iuc	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat	5.2.3	cat	5.3	(5/5)	(2/5)	(5/5)
@@ -544,7 +546,7 @@ cdhit	8278.0	6.0	cd_hit	Cluster or compare biological sequence datasets	cd-hit	c
 cemitool	98.0	9.0	cemitool	Gene co-expression network analysis tool	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	1.18.1	bioconductor-cemitool	1.26.0	(1/1)	(0/1)	(1/1)
 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/	1.0.1	r-getopt		(0/1)	(0/1)	(0/1)
 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 provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Operation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics	To update	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	1.2.0	checkm-genome	1.2.2	(0/10)	(0/10)	(10/10)
-cherri			cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	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.			To update	https://github.com/BackofenLab/Cherri	Transcriptomics, RNA		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cherri	0.7	cherri	0.8	(0/2)	(0/2)	(2/2)
+cherri			cherri_eval, cherri_train	Computational Help Evaluating RNA-RNA interactions	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	0.7	cherri	0.8	(0/2)	(0/2)	(2/2)
 chira	74.0		chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify	Chimeric Read Annotator for RNA-RNA interactome data	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	1.4.3	chira	1.4.3	(5/5)	(0/5)	(5/5)
 chopin2			chopin2	Domain-Agnostic Supervised Learning with Hyperdimensional Computing						To update	https://github.com/cumbof/chopin2	Machine Learning	chopin2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/chopin2	1.0.7	chopin2		(1/1)	(0/1)	(0/1)
 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	1.5.a	chromeister	1.5.a	(0/1)	(1/1)	(1/1)
@@ -556,7 +558,7 @@ clustalw	46793.0	651.0	clustalw	ClustalW multiple sequence alignment program for
                 clustal2
             "					Up-to-date	http://www.clustal.org/clustal2/	Phylogenetics, Sequence Analysis	clustalw	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw	2.1	clustalw	2.1	(1/1)	(1/1)	(1/1)
 cnvkit			cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_breaks, cnvkit_call, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_reference, cnvkit_scatter, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target	detecting copy number variants and alterations genome-wide from high-throughput sequencing	cnvkit	CNVkit	CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data.	Variant calling	DNA structural variation	Up-to-date	https://github.com/etal/cnvkit	Variant Analysis	cnvkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit	0.9.10	cnvkit	0.9.10	(0/17)	(0/17)	(17/17)
-codeml	60901.0	29.0	codeml	Detects positive selection						To update	http://abacus.gene.ucl.ac.uk/software/paml.html	Phylogenetics	codeml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml	4.9	paml	4.10.7	(0/1)	(0/1)	(1/1)
+codeml	60901.0	29.0	codeml	Detects positive selection	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	4.9	paml	4.10.7	(0/1)	(0/1)	(1/1)
 cojac			cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	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	0.9.1	cojac	0.9.1	(2/3)	(0/3)	(3/3)
 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	24.7.14+galaxy0	commet	24.7.14	(0/7)	(0/7)	(1/7)
 collection_column_join	20857.0	1483.0	collection_column_join	Column Join on Collections						To update		Text Manipulation	collection_column_join	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join	0.0.3	coreutils	8.25	(1/1)	(1/1)	(1/1)
@@ -595,7 +597,7 @@ dimet			dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECU
 disco	369.0	42.0	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	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/		disco	1.2	(1/1)	(0/1)	(1/1)
 dnabot			dnabot	DNA assembly using BASIC on OpenTrons						To update	https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT	Synthetic Biology	dnabot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnabot	3.1.0	dnabot		(0/1)	(0/1)	(0/1)
 dnaweaver			dnaweaver	Given a SBOL input, calculate assembly parts for Gibson or Golden Gate.						Up-to-date	https://github.com/Edinburgh-Genome-Foundry/DnaWeaver	Synthetic Biology	dnaweaver	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dnaweaver	1.0.2	dnaweaver_synbiocad	1.0.2	(0/1)	(0/1)	(0/1)
-dram			dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function						To update	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	1.3.5	dram	1.4.6	(0/5)	(0/5)	(5/5)
+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	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	1.3.5	dram	1.4.6	(0/5)	(0/5)	(5/5)
 drep			drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	3.4.5	drep	3.4.5	(0/2)	(0/2)	(2/2)
 dropletutils	3934.0	126.0	dropletutils	DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data	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/	1.10.0	bioconductor-dropletutils	1.22.0	(1/1)	(1/1)	(1/1)
 ebi_tools			ebi_metagenomics_run_downloader, ebi_search_rest_results	Tools to query and download data from several EMBL-EBI databases						To update	http://www.ebi.ac.uk/services/all	Web Services, Data Source	ebi_tools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools	0.1.0	six		(2/2)	(0/2)	(2/2)
@@ -608,9 +610,9 @@ ensembl_vep	2653.0	119.0	ensembl_vep	Ensembl VEP: Annotate VCFs with variant eff
 episcanpy			episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess	EpiScanpy – Epigenomics single cell analysis in python	episcanpy	epiScanpy	Epigenomics Single Cell Analysis in Python.	Enrichment analysis, Imputation	Epigenomics, Cell biology, DNA	To update	https://github.com/colomemaria/epiScanpy	Epigenetics	episcanpy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/	0.3.2	episcanpy	0.4.0	(2/3)	(0/3)	(3/3)
 exomedepth	410.0	29.0	exomedepth	ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data	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	1.1.0	r-exomedepth	1.1.16	(1/1)	(0/1)	(1/1)
 exonerate	988.0	59.0	exonerate	Exonerate is a generic tool for pairwise sequence comparison.	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	2.4.0	exonerate	2.4.0	(1/1)	(1/1)	(1/1)
-export2graphlan	5265.0	200.0	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn						To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	0.20	export2graphlan	0.22	(1/1)	(1/1)	(1/1)
+export2graphlan	5265.0	200.0	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	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/	0.20	export2graphlan	0.22	(1/1)	(1/1)	(1/1)
 extract_genomic_dna	11348.0	285.0	Extract genomic DNA 1	Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes.						To update		Genomic Interval Operations	extract_genomic_dna	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/extract_genomic_dna	3.0.3+galaxy2	bx-python	0.10.0	(1/1)	(0/1)	(1/1)
-fargene	459.0	52.0	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )						Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	0.1	fargene	0.1	(1/1)	(0/1)	(1/1)
+fargene	459.0	52.0	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	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	0.1	fargene	0.1	(1/1)	(0/1)	(1/1)
 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	1.0.1	openjdk		(1/1)	(0/1)	(1/1)
 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/	2.0	numpy		(1/1)	(1/1)	(1/1)
 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		1.3	fastani	1.34	(0/1)	(0/1)	(1/1)
@@ -618,7 +620,7 @@ fastp	1055760.0	2803.0	fastp	Fast all-in-one preprocessing for FASTQ files	"
                 fastp
             "					To update	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp		fastp	0.23.4	(1/1)	(1/1)	(1/1)
 fastqc	1556625.0	17447.0	fastqc	Read QC reports using FastQC	fastqc	FastQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.	Sequence composition calculation, Sequencing quality control, Statistical calculation	Sequencing, Data quality management, Sequence analysis	To update	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Fastq Manipulation	fastqc	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc	0.74+galaxy0	fastqc	0.12.1	(1/1)	(1/1)	(1/1)
-fastqe	4333.0	1266.0	fastqe	FASTQE						To update	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	(1/1)	(1/1)	(1/1)
+fastqe	4333.0	1266.0	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	0.3.1+galaxy0	fastqe	0.3.1	(1/1)	(1/1)	(1/1)
 fasttree	55434.0	379.0	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	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	2.1.10	fasttree	2.1.11	(1/1)	(1/1)	(1/1)
 featurecounts	696399.0	4679.0	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	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	Sequencing	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	2.0.3	subread	2.0.6	(1/1)	(1/1)	(1/1)
 feelnc	1191.0	46.0	feelnc	Galaxy wrapper for 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	0.2.1	feelnc	0.2	(1/1)	(0/1)	(1/1)
@@ -632,7 +634,7 @@ flash	13759.0	74.0	flash	Fast Length Adjustment of SHort reads	flash	FLASH	Ident
 fraggenescan	1102.0	68.0	fraggenescan	Tool for finding (fragmented) genes in short read	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/		fraggenescan	1.31	(0/1)	(1/1)	(1/1)
 freebayes	153548.0	3059.0	freebayes, bamleftalign	Galaxy Freebayes Bayesian genetic variant detector tool	freebayes	FreeBayes	Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.	Variant calling, Statistical calculation	Genomics, Genetic variation, Rare diseases	To update	https://github.com/ekg/freebayes	Variant Analysis	freebayes	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes	1.3.6	freebayes	1.3.7	(2/2)	(2/2)	(2/2)
 freec			control_freec	Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH.	freec	FREEC	A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies.	Copy number estimation, Variant calling, Genome alignment	DNA structural variation, Oncology, Human genetics, Data mining	To update	http://boevalab.inf.ethz.ch/FREEC/	Variant Analysis	control_freec	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freec	11.6	gawk		(0/1)	(0/1)	(1/1)
-freyja			freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja					To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	1.4.4	freyja	1.4.8	(2/4)	(0/4)	(4/4)
+freyja			freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja					To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	1.4.4	freyja	1.4.9	(2/4)	(0/4)	(4/4)
 fsd			fsd, fsd_beforevsafter, fsd_regions, td	Tool that plots a histogram of sizes of read families						To update		Graphics	duplex_family_size_distribution	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd	1.0.2	matplotlib		(4/4)	(0/4)	(0/4)
 funannotate			funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	"
                 funannotate
@@ -654,20 +656,20 @@ gfa_to_fa	8274.0	332.0	gfa_to_fa	gfa_to_fa - Converting GFA format to Fasta form
 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	1.2	bcbiogff	0.6.6	(1/1)	(1/1)	(1/1)
 gffcompare	3477.0	381.0	gffcompare	Galaxy wrappers for Geo Pertea's GffCompare package.	gffcompare	gffcompare	Program for comparing, annotating, merging and tracking transcripts in GFF files.	Sequence annotation	Nucleic acids, Sequence analysis	Up-to-date	https://github.com/gpertea/gffcompare/	Transcriptomics	gffcompare	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare	0.12.6	gffcompare	0.12.6	(1/1)	(1/1)	(1/1)
 gffread	10995.0	680.0	gffread	gffread filters and/or converts GFF3/GTF2 records	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	0.12.7	gffread	0.12.7	(1/1)	(1/1)	(1/1)
-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	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	3.4.0	r-base		(5/5)	(2/5)	(5/5)
+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	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	3.4.0	r-base		(5/5)	(5/5)	(5/5)
 ggupset			emc-ggupset	Create Upset Plots with ggupset						To update	https://github.com/const-ae/ggupset	Graphics	ggupset	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggupset	1.0	r-ggupset		(0/1)	(0/1)	(0/1)
 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 (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		glimmer	3.02	(0/8)	(0/8)	(4/8)
 goenrichment	5206.0	321.0	goenrichment, goslimmer	Performs GO Enrichment analysis.	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 Ciência.	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	2.0.1	goenrichment	2.0.1	(2/2)	(2/2)	(2/2)
 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	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	1.50.0	bioconductor-goseq	1.54.0	(1/1)	(1/1)	(1/1)
 gprofiler			gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense	functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more						To update	https://biit.cs.ut.ee/gprofiler	Statistics, Web Services	gprofiler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/	@TOOL_VERSION@+galaxy11	r-gprofiler2		(5/5)	(0/5)	(5/5)
 graphembed	63.0	2.0	graphembed	Compute a 2D embedding of a data matrix given supervised class information						Up-to-date	https://github.com/fabriziocosta/GraphEmbed	Statistics, Graphics	graphembed	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/graphembed/	2.4	graph_embed	2.4	(1/1)	(0/1)	(1/1)
-graphlan	5002.0	247.0	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees						To update	https://bitbucket.org/nsegata/graphlan/overview	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/		graphlan	1.1.3	(2/2)	(2/2)	(2/2)
-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. 						To update	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	2.2.2	gtdbtk	2.3.2	(0/1)	(1/1)	(0/1)
+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 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/		graphlan	1.1.3	(2/2)	(2/2)	(2/2)
+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	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	2.2.2	gtdbtk	2.3.2	(0/1)	(1/1)	(0/1)
 gtfToBed12			gtftobed12	Convert GTF files to BED12 format	UCSC_Genome_Browser_Utilities	UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README	Convert Formats	gtftobed12	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12	357	ucsc-gtftogenepred	447	(1/1)	(1/1)	(1/1)
 gubbins	3340.0	145.0	gubbins	Gubbins - bacterial recombination detection	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	3.2.1	gubbins	3.3.3	(1/1)	(1/1)	(1/1)
 gvcftools			gvcftools_extract_variants							To update	https://github.com/sequencing/gvcftools	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gvcftools	0.1	gvcftools	0.17.0	(0/1)	(0/1)	(0/1)
 gwastools			gwastools_manhattan_plot		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		0.1.0	bioconductor-gwastools	1.48.0	(0/1)	(0/1)	(0/1)
-hamronization			hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.						To update	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	1.0.3	hamronization	1.1.4	(0/2)	(0/2)	(2/2)
+hamronization			hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	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	To update	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	1.0.3	hamronization	1.1.4	(0/2)	(0/2)	(2/2)
 hansel			bio_hansel	Heidelberg and Enteritidis SNP Elucidation	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	2.6.1	bio_hansel	2.6.1	(1/1)	(0/1)	(1/1)
 hapcut2			hapcut2	Robust and accurate haplotype assembly for diverse sequencing technologies	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	1.3.3	hapcut2	1.3.3	(0/1)	(1/1)	(0/1)
 hapog	295.0	36.0	hapog	Hapo-G - Haplotype-Aware Polishing of Genomes	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	1.3.7	hapog	1.3.7	(0/1)	(0/1)	(1/1)
@@ -676,17 +678,17 @@ heatmap2			ggplot2_heatmap2	heatmap.2 function from the R gplots package						To
 heinz	1186.0	242.0	heinz_bum, heinz, heinz_scoring, heinz_visualization	An algorithm for identification of the optimal scoring subnetwork.	bionet	BioNet	This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from these p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.	Protein interaction analysis	Molecular interactions, pathways and networks, Protein interactions	To update	https://github.com/ls-cwi/heinz	Transcriptomics, Visualization, Statistics	heinz	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/heinz	1.0	bioconductor-bionet	1.62.0	(4/4)	(4/4)	(4/4)
 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	3.7.2	hicexplorer	3.7.3	(0/40)	(5/40)	(40/40)
 hicstuff			hicstuff_pipeline							To update	https://github.com/koszullab/hicstuff	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicstuff	3.1.5	hicstuff	3.2.1	(0/1)	(0/1)	(0/1)
-hifiasm_meta	137.0	12.0	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.						To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	(0/1)	(1/1)	(1/1)
+hifiasm_meta	137.0	12.0	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	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	0.3.1	hifiasm_meta	hamtv0.3.1	(0/1)	(1/1)	(1/1)
 hisat2	299104.0	4183.0	hisat2	HISAT2 is a fast and sensitive spliced alignment program.	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	2.2.1	hisat2	2.2.1	(1/1)	(1/1)	(1/1)
 hivclustering			hivclustering	Infers transmission networks from pairwise distances inferred by tn93						To update	https://pypi.org/project/hivclustering/	Next Gen Mappers	hivclustering	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hivclustering/	1.3.1	python-hivclustering	1.6.8	(0/1)	(0/1)	(0/1)
 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	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	To update	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	3.3.2	hmmer	3.4	(0/12)	(12/12)	(12/12)
 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 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	4.11	homer	4.11	(0/5)	(0/5)	(5/5)
 htseq_count	154533.0	1419.0	htseq_count	Count aligned reads (SAM/BAM) that overlap genomic features (GFF)	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	2.0.5	htseq	2.0.5	(1/1)	(1/1)	(1/1)
-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 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	3.8	humann	3.8	(6/13)	(6/13)	(13/13)
+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 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	3.8	humann	3.8	(6/13)	(10/13)	(13/13)
 hybpiper			hybpiper	Analyse targeted sequence capture data	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	Up-to-date	https://github.com/mossmatters/HybPiper	Sequence Analysis, Phylogenetics	hybpiper	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hybpiper	2.1.6	hybpiper	2.1.6	(0/1)	(1/1)	(0/1)
 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	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/	2.5.47	hyphy	2.5.59	(17/17)	(2/17)	(17/17)
 hypo	354.0	39.0	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	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	1.0.3	hypo	1.0.3	(0/1)	(0/1)	(1/1)
-icescreen			icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.						Up-to-date	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	1.3.1	icescreen	1.3.1	(0/1)	(0/1)	(0/1)
+icescreen			icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	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	Up-to-date	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	1.3.1	icescreen	1.3.1	(0/1)	(0/1)	(0/1)
 idba_ud	721.0	43.0	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	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		idba	1.1.3	(3/3)	(0/3)	(3/3)
 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/	2.0.3	idr	2.0.4.2	(1/1)	(0/1)	(1/1)
 idr_download			idr_download_by_ids	Image Data Resource downloading tool						To update	https://idr.openmicroscopy.org	Data Source	idr_download_by_ids	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idr_download	0.44.1	omero-py	5.11.1	(0/1)	(0/1)	(1/1)
@@ -706,7 +708,7 @@ iwtomics			iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot	In
 jasminesv	30.0	3.0	jasminesv	Merge structural variants across samples						To update	https://github.com/mkirsche/Jasmine/	Variant Analysis	jasminesv	iuc	https://github.com/galaxyproject/tools-iuc/jasminesv/	1.0.11	jasminesv	1.1.5	(1/1)	(0/1)	(1/1)
 jbrowse	18229.0	2346.0	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	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	1.16.11	jbrowse	1.16.11	(2/2)	(2/2)	(2/2)
 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	0.8.4	jcvi	1.3.9	(1/1)	(1/1)	(1/1)
-jellyfish	1138.0	91.0	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	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		kmer-jellyfish	2.3.0	(0/1)	(1/1)	(1/1)
+jellyfish	1138.0	91.0	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	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		kmer-jellyfish	2.3.1	(0/1)	(1/1)	(1/1)
 join_files_by_id			join_files_by_id	This tool will join datasets according to a column with identifier						To update		Text Manipulation	join_files_by_id	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id	1.0	r-data.table	1.11.6	(0/1)	(0/1)	(0/1)
 jq	2312.0	21.0	jq	JQ is a lightweight and flexible command-line JSON processor						To update	https://stedolan.github.io/jq/	Text Manipulation	jq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jq	1.0	jq	1.5	(1/1)	(1/1)	(1/1)
 jvarkit			jvarkit_wgscoverageplotter	Jvarkit : Java utilities for Bioinformatics						Up-to-date	https://lindenb.github.io/jvarkit/	SAM	jvarkit	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit	20201223	jvarkit-wgscoverageplotter	20201223	(1/1)	(0/1)	(1/1)
@@ -719,14 +721,14 @@ kma			kma_map	Map with KMA						To update	https://bitbucket.org/genomicepidemiol
 kofamscan	594.0	33.0	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model						Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	1.3.0	kofamscan	1.3.0	(0/1)	(0/1)	(1/1)
 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	1.2.0	kraken-biom	1.2.0	(0/1)	(1/1)	(1/1)
 kraken_taxonomy_report	2527.0	354.0	kraken_taxonomy_report	Kraken taxonomy report						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	0.0.3	biopython	1.70	(1/1)	(0/1)	(1/1)
-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 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	1.2	krakentools	1.2	(1/6)	(2/6)	(6/6)
+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 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	1.2	krakentools	1.2	(1/6)	(4/6)	(6/6)
 krocus			krocus	Predict MLST directly from uncorrected long reads						To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	1.0.1	krocus	1.0.3	(0/1)	(0/1)	(0/1)
-last	227.0	41.0	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	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	1205	last	1540	(0/5)	(0/5)	(5/5)
+last	227.0	41.0	last_al, last_db, last_split, last_train, last_maf_convert	LAST finds similar regions between sequences.	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	1205	last	1541	(0/5)	(0/5)	(5/5)
 lastz	83331.0	188.0	lastz_wrapper_2, lastz_d_wrapper	Galaxy wrappers for the Lastz and Lastz_d	lastz	LASTZ	A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.	Sequence alignment, Read mapping	Genomics	Up-to-date	https://github.com/lastz/lastz	Next Gen Mappers	lastz	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz	1.04.22	lastz	1.04.22	(2/2)	(2/2)	(2/2)
 lcrgenie			lcrgenie	Ligase Chain Reaction Genie						To update	https://github.com/neilswainston/LCRGenie	Synthetic Biology	lcrgenie	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lcrgenie	1.0.2	lcr_genie		(0/1)	(0/1)	(0/1)
 legsta	55.0	7.0	legsta	Performs in silico Legionella pneumophila sequence based typing.						Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	0.5.1	legsta	0.5.1	(0/1)	(0/1)	(1/1)
 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	0.1.2	r-optparse	1.3.2	(1/1)	(1/1)	(1/1)
-limma_voom	20344.0	1012.0	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	To update	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	3.50.1	bioconductor-limma	3.58.1	(1/1)	(1/1)	(1/1)
+limma_voom	20344.0	1012.0	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	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	3.58.1	bioconductor-limma	3.58.1	(1/1)	(1/1)	(1/1)
 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 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	1.4.0	r-base		(0/1)	(0/1)	(1/1)
 links	405.0	77.0	links	Scaffold genome assemblies with long reads.	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	2.0.1	links	2.0.1	(0/1)	(1/1)	(1/1)
 lofreq			lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi	LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering.						Up-to-date	https://csb5.github.io/lofreq/	Variant Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq	2.1.5	lofreq	2.1.5	(5/5)	(5/5)	(5/5)
@@ -793,7 +795,7 @@ nextclade	3527.0	169.0	nextalign, nextclade	Identify differences between your se
 ngmlr	1266.0	21.0	ngmlr	CoNvex Gap-cost alignMents for Long Reads	ngmlr	NGMLR	An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation.	DNA mapping, Sequence alignment, Genetic variation analysis	Sequencing, Mapping, DNA structural variation	Up-to-date	https://github.com/philres/ngmlr	Next Gen Mappers	ngmlr	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngmlr	0.2.7	ngmlr	0.2.7	(0/1)	(0/1)	(1/1)
 ngsutils			ngsutils_bam_filter	NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed.	ngsutils	NGSUtils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets	Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering	Genomics, Transcriptomics	To update	https://github.com/ngsutils/ngsutils	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils		ngsutils	0.5.9	(1/1)	(1/1)	(1/1)
 nonpareil	142.0	5.0	nonpareil	Estimate average coverage in metagenomic datasets						To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	3.1.1	nonpareil	3.4.1	(1/1)	(0/1)	(1/1)
-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	4.3.1	novoplasty	4.3.3	(0/1)	(1/1)	(1/1)
+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	4.3.1	novoplasty	4.3.5	(0/1)	(1/1)	(1/1)
 nugen_nudup			nugen_nudup	Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products.						Up-to-date	http://nugentechnologies.github.io/nudup/	SAM, Metagenomics, Sequence Analysis, Transcriptomics	nugen_nudup	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup	2.3.3	nudup	2.3.3	(0/1)	(0/1)	(0/1)
 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	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	1.2.13	obitools	1.2.13	(0/10)	(10/10)	(10/10)
 ococo	1877.0	32.0	ococo	Variant detection of SNVs						Up-to-date	https://github.com/karel-brinda/ococo	Variant Analysis	ococo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ococo	0.1.2.6	ococo	0.1.2.6	(1/1)	(0/1)	(1/1)
@@ -817,11 +819,11 @@ pharokka	2565.0	74.0	pharokka	rapid standardised annotation tool for bacteriopha
             "					To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	"
                 pharokka
             "		(0/1)	(1/1)	(1/1)
-phyloseq			phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data						To update	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	1.38.0	bioconductor-phyloseq	1.46.0	(0/3)	(0/3)	(3/3)
+phyloseq			phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	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	To update	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	1.38.0	bioconductor-phyloseq	1.46.0	(0/3)	(0/3)	(3/3)
 phyml	1770.0	104.0	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	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	3.3.20220408	phyml	3.3.20220408	(0/1)	(1/1)	(1/1)
 picard	379429.0	3956.0	picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile	Picard SAM/BAM manipulation tools.	picard_fastqtosam	picard_fastqtosam	Create an unaligned BAM file.	Formatting	Sequencing	To update	http://broadinstitute.github.io/picard/	SAM	picard	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard	2.18.2	picard	3.1.1	(31/31)	(31/31)	(31/31)
 pick_value	116.0	2.0	pick_value	Compose a text parameter value using text, integer and float values						To update		Text Manipulation	pick_value	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value	0.2.0			(1/1)	(0/1)	(1/1)
-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						To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	1.1.1	picrust	1.1.4	(0/6)	(6/6)	(5/6)
+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 (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	1.1.1	picrust	1.1.4	(0/6)	(6/6)	(5/6)
 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 (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	2.5.1	picrust2	2.5.2	(0/7)	(7/7)	(7/7)
 pilon	7942.0	467.0	pilon	pilon is a tool for assembly improvement and variant analysis in bacteria	pilon	pilon	Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.	Sequence assembly, Analysis, Read alignment	Assembly	To update		Variant Analysis	pilon	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon	1.20.1	pilon	1.24	(1/1)	(1/1)	(1/1)
 pipelign	983.0	83.0	pipelign	Multipe sequence alignment						Up-to-date	https://github.com/asmmhossain/pipelign/	Next Gen Mappers	pipelign	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign	0.2	pipelign	0.2	(1/1)	(0/1)	(1/1)
@@ -862,7 +864,7 @@ raven	6902.0	262.0	raven	Raven is a de novo genome assembler for long uncorrecte
 raxml	6808.0	383.0	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	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	8.2.12	raxml	8.2.13	(1/1)	(1/1)	(1/1)
 rcorrector	569.0	30.0	rcorrector	Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.	rcorrector	Rcorrector	This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing.	Sequencing error detection	RNA, RNA-Seq, Sequencing	To update	https://github.com/mourisl/Rcorrector	Fastq Manipulation	rcorrector	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rcorrector	1.0.3+galaxy1	rcorrector	1.0.6	(0/1)	(0/1)	(1/1)
 read_it_and_keep	3370.0	71.0	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads						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	0.2.2	read-it-and-keep	0.3.0	(1/1)	(0/1)	(1/1)
-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	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	1.13.2	recentrifuge	1.13.2	(0/1)	(0/1)	(1/1)
+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	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	To update	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	1.13.2	recentrifuge	1.14.0	(0/1)	(0/1)	(1/1)
 red	578.0	88.0	red	Red (REpeat Detector)						Up-to-date	https://github.com/BioinformaticsToolsmith/Red	Sequence Analysis	red	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/red	2018.09.10	red	2018.09.10	(1/1)	(1/1)	(1/1)
 repeatmasker			repeatmasker_wrapper	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.	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	4.1.5	repeatmasker	4.1.5	(1/1)	(1/1)	(1/1)
 repeatmodeler	1177.0	217.0	repeatmodeler	RepeatModeler - Model repetitive DNA						To update	https://www.repeatmasker.org/RepeatModeler/	Genome annotation	repeatmodeler	csbl	https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler	2.0.5			(1/1)	(1/1)	(1/1)
@@ -870,7 +872,7 @@ repmatch_gff3			repmatch_gff3	Contains a tool that matches corresponding peak-pa
 reshape2			cast, melt	Flexibly restructure and aggregate data using just the two functions melt and dcast						To update	https://cran.r-project.org/web/packages/reshape2/index.html	Text Manipulation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/reshape2	1.4.2	r-reshape2		(2/2)	(0/2)	(2/2)
 resize_coordinate_window	85.0	5.0	resize_coordinate_window	Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size.						To update		Genomic Interval Operations	resize_coordinate_window	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window	1.0.2	python		(1/1)	(0/1)	(1/1)
 rgcca	44.0	3.0	rgcca	multi-block analysis						To update	https://github.com/rgcca-factory/RGCCA	Statistics	rgcca	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgcca	3.0.2	rgccacmd	3.0.3	(1/1)	(0/1)	(1/1)
-rgrnastar	416677.0	3843.0	rna_star, rna_starsolo	RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper	star	STAR	Ultrafast universal RNA-seq data aligner	Sequence alignment	RNA-Seq, Transcriptomics	To update	https://github.com/alexdobin/STAR	Next Gen Mappers, Transcriptomics	rgrnastar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar	2.7.10b	star	2.7.11b	(2/2)	(2/2)	(2/2)
+rgrnastar	416677.0	3843.0	rna_star, rna_starsolo	RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper	star	STAR	Ultrafast universal RNA-seq data aligner	Sequence alignment	RNA-Seq, Transcriptomics	To update	https://github.com/alexdobin/STAR	Next Gen Mappers, Transcriptomics	rgrnastar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar	2.7.11a	star	2.7.11b	(2/2)	(2/2)	(2/2)
 ribowaltz			ribowaltz_process, ribowaltz_plot	Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data	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	1.2.0	ribowaltz	2.0	(0/2)	(0/2)	(2/2)
 rnaquast	1110.0	109.0	rna_quast	rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies.	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	2.2.3	rnaquast	2.2.3	(0/1)	(0/1)	(1/1)
 roary	12225.0	656.0	roary	Roary the pangenome pipeline	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	3.13.0	roary	3.13.0	(1/1)	(1/1)	(1/1)
@@ -958,10 +960,10 @@ tetyper	69.0	8.0	tetyper	Type a specific transposable element (TE) of interest f
 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/	1.0.6	tn93	1.0.13	(4/4)	(0/4)	(4/4)
 tracy			tracy_align, tracy_assemble, tracy_basecall, tracy_decompose							To update				iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy	0.6.1	tracy	0.7.6	(0/4)	(0/4)	(4/4)
 transdecoder	5468.0	348.0	transdecoder	TransDecoder finds coding regions within transcripts	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	5.5.0	transdecoder	5.7.1	(1/1)	(1/1)	(1/1)
-transit			gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	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/	3.0.2	transit	3.2.3	(5/5)	(2/5)	(5/5)
+transit			gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	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/	3.0.2	transit	3.2.3	(5/5)	(4/5)	(5/5)
 transtermhp	229.0	5.0	transtermhp	Finds rho-independent transcription terminators in bacterial genomes						To update		Sequence Analysis	transtermhp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp		transtermhp	2.09	(1/1)	(0/1)	(1/1)
 trimmomatic	305866.0	5862.0	trimmomatic	A flexible read trimming tool for Illumina NGS data						Up-to-date	http://www.usadellab.org/cms/?page=trimmomatic	Fastq Manipulation	trimmomatic	pjbriggs	https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic	0.39	trimmomatic	0.39	(1/1)	(1/1)	(1/1)
-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 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	2.15.1	trinity	2.15.1	(8/13)	(11/13)	(13/13)
+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 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	2.15.1	trinity	2.15.1	(8/13)	(12/13)	(13/13)
 trinotate	1796.0	151.0	trinotate	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes.	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	3.2.2	trinotate	4.0.2	(1/1)	(1/1)	(1/1)
 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	0.5.4	trycycler	0.5.4	(0/5)	(5/5)	(5/5)
 tsebra	5.0		tsebra	This tool has been developed to combine BRAKER predictions.						To update	https://github.com/Gaius-Augustus/TSEBRA	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra	1.1.2	tsebra	1.1.2.2	(0/1)	(0/1)	(1/1)
@@ -970,16 +972,16 @@ tximport	1408.0	88.0	tximport	Wrapper for the Bioconductor package tximport	txim
 ucsc_blat			ucsc_blat	Standalone blat sequence search command line tool	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		377	ucsc-blat	445	(0/1)	(0/1)	(0/1)
 fasplit			fasplit	faSplit is a tool to split a single FASTA file into several files	UCSC_Genome_Browser_Utilities	UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Fasta Manipulation	ucsc_fasplit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fasplit	377	ucsc-fasplit	377	(1/1)	(1/1)	(1/1)
 fatovcf			fatovcf	Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs	UCSC_Genome_Browser_Utilities	UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	http://hgdownload.cse.ucsc.edu/admin/exe/	Convert Formats	ucsc_fatovcf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/fatovcf	448	ucsc-fatovcf	448	(1/1)	(0/1)	(1/1)
-twobittofa			ucsc-twobittofa	twoBitToFa is a tool to convert all or part of .2bit file to FASTA	UCSC_Genome_Browser_Utilities	UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	https://genome.ucsc.edu/goldenpath/help/twoBit.html	Convert Formats	ucsc_twobittofa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa	377	ucsc-twobittofa	455	(1/1)	(0/1)	(1/1)
+twobittofa			ucsc-twobittofa	twoBitToFa is a tool to convert all or part of .2bit file to FASTA	UCSC_Genome_Browser_Utilities	UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	To update	https://genome.ucsc.edu/goldenpath/help/twoBit.html	Convert Formats	ucsc_twobittofa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ucsc-tools/twobittofa	377	ucsc-twobittofa	455	(1/1)	(1/1)	(1/1)
 wigtobigwig			ucsc_wigtobigwig	converts bedGraph (wig) files into binary bigwig	UCSC_Genome_Browser_Utilities	UCSC Genome Browser Utilities	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		Sequence analysis	Up-to-date	https://genome.ucsc.edu/goldenPath/help/bigWig.html	Convert Formats	ucsc_wigtobigwig	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/wigtobigwig	447	ucsc-wigtobigwig	447	(0/1)	(0/1)	(1/1)
-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	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	1.1.2	umi_tools	1.1.4	(5/5)	(3/5)	(5/5)
+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	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	1.1.2	umi_tools	1.1.4	(5/5)	(5/5)	(5/5)
 unicycler	65732.0	1558.0	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	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	0.5.0	unicycler	0.5.0	(1/1)	(1/1)	(1/1)
 usher	1060.0	5.0	usher_matutils, usher	UShER toolkit wrappers						To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	0.2.1	usher	0.6.3	(0/2)	(0/2)	(2/2)
 valet	637.0	20.0	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.						To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet		valet	1.0	(1/1)	(0/1)	(1/1)
 vapor	3164.0	94.0	vapor	Classify Influenza samples from raw short read sequence data	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	1.0.2	vapor	1.0.2	(1/1)	(0/1)	(1/1)
 vardict			vardict_java	VarDict - calls SNVs and indels for tumour-normal pairs						To update	https://github.com/AstraZeneca-NGS/VarDictJava	Variant Analysis	vardict_java	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict	1.8.3	python		(0/1)	(0/1)	(1/1)
 variant_analyzer	88.0	3.0	mut2read, mut2sscs, read2mut	Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data						To update		Variant Analysis	variant_analyzer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer	2.0.0	matplotlib		(3/3)	(0/3)	(3/3)
-varscan	208.0	16.0	varscan_copynumber, varscan_mpileup, varscan_somatic	VarScan is a variant caller for high-throughput sequencing data						To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/varscan	2.4.3	varscan	2.4.6	(3/3)	(1/3)	(3/3)
+varscan	208.0	16.0	varscan_copynumber, varscan_mpileup, varscan_somatic	VarScan is a variant caller for high-throughput sequencing data						To update	https://dkoboldt.github.io/varscan/	Variant Analysis	varscan	iuc	https://github.com/galaxyproject/iuc/tree/master/tools/varscan	2.4.3	varscan	2.4.6	(3/3)	(2/3)	(3/3)
 varvamp			varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	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	1.1.1	varvamp	1.1.1	(0/1)	(0/1)	(1/1)
 vcf2maf	751.0	29.0	vcf2maf	vcf2maf: Convert VCF into MAF						Up-to-date		Convert Formats	vcf2maf	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf	1.6.21	vcf2maf	1.6.21	(0/1)	(1/1)	(1/1)
 vcfanno	872.0	87.0	vcfanno	Annotate VCF files	vcfanno	vcfanno	Fast, flexible annotation of genetic variants.	SNP annotation	Genetic variation, Data submission, annotation and curation	To update	https://github.com/brentp/vcfanno	Variant Analysis	vcfanno	iuc	https://github.com/galaxyproject/tools-iuc/vcfanno/	0.3.3	vcfanno	0.3.5	(0/1)	(0/1)	(1/1)
@@ -987,7 +989,7 @@ vegan			vegan_diversity, vegan_fisher_alpha, vegan_rarefaction							To update	h
 velocyto			velocyto_cli	Velocyto is a library for the analysis of RNA velocity.						Up-to-date	http://velocyto.org/	Transcriptomics	velocyto	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto	0.17.17	velocyto.py	0.17.17	(1/1)	(0/1)	(1/1)
 velvet	12218.0	1280.0	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	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		velvet	1.2.10	(2/2)	(2/2)	(2/2)
 velvet_optimiser			velvetoptimiser	Automatically optimize Velvet assemblies	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	2.2.6+galaxy2	velvet	1.2.10	(1/1)	(1/1)	(1/1)
-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	1.3.1	verkko	1.4.1	(0/1)	(0/1)	(1/1)
+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	1.3.1	verkko	2.0	(0/1)	(0/1)	(1/1)
 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	1.23.0	vg	1.54.0	(0/3)	(0/3)	(3/3)
 virhunter	234.0	40.0	virhunter	Deep Learning method for novel virus detection in sequencing data	virhunter	VirHunter	VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination).	Sequence classification	Virology	To update	https://github.com/cbib/virhunter	Machine Learning	virhunter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter	1.0.0	numpy		(0/1)	(0/1)	(1/1)
 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	0.0.5	r-ggplot2	2.2.1	(1/1)	(1/1)	(1/1)
@@ -1002,7 +1004,7 @@ yahs	344.0	64.0	yahs	Yet Another Hi-C scaffolding tool						Up-to-date	https://g
 zerone	90.0	2.0	zerone	ChIP-seq discretization and quality control						Up-to-date	https://github.com/nanakiksc/zerone	ChIP-seq	zerone	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/zerone	1.0	zerone	1.0	(0/1)	(0/1)	(1/1)
 bamtools	14039.0	208.0	bamtools	Operate on and transform BAM datasets in various ways using bamtools						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	2.5.2	bamtools	2.5.2	(1/1)	(0/1)	(1/1)
 bamtools_filter	114845.0	1195.0	bamFilter	Filter BAM datasets on various attributes using bamtools filter						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	2.5.2	bamtools	2.5.2	(1/1)	(1/1)	(1/1)
-bamtools_split	1434.0	47.0	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag							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	2.5.2	bamtools	2.5.2	(4/4)	(0/4)	(4/4)
+bamtools_split	1434.0	47.0	bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag							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	2.5.2	bamtools	2.5.2	(4/4)	(2/4)	(4/4)
 biotradis			bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.						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	1.4.5	biotradis	1.4.5	(3/3)	(0/3)	(0/3)
 cuffcompare	1130.0	65.0	cuffcompare	Galaxy wrappers for the Cuffcompare tool.						Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffcompare	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare	2.2.1	cufflinks	2.2.1	(1/1)	(1/1)	(1/1)
 cuffdiff	5831.0	228.0	cuffdiff	Galaxy wrappers for the Cuffdiff tool.						Up-to-date	http://cole-trapnell-lab.github.io/cufflinks/	Transcriptomics	cuffdiff	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff	2.2.1	cufflinks	2.2.1	(1/1)	(0/1)	(1/1)
@@ -1041,7 +1043,7 @@ fastq_trimmer	9757.0	210.0	fastq_trimmer	FASTQ Trimmer by quality						Up-to-dat
 fastqtofasta	178172.0	1371.0	fastq_to_fasta_python	FASTQ to FASTA converter						Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	fastqtofasta	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta	1.1.5	galaxy_sequence_utils	1.1.5	(1/1)	(1/1)	(1/1)
 tabular_to_fastq	7388.0	200.0	tabular_to_fastq	Tabular to FASTQ converter						Up-to-date	https://github.com/galaxyproject/sequence_utils	Fastq Manipulation	tabular_to_fastq	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq	1.1.5	galaxy_sequence_utils	1.1.5	(1/1)	(1/1)	(1/1)
 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.						To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken	devteam	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/		kraken	1.1.1	(5/5)	(5/5)	(5/5)
-kraken2	185308.0	2367.0	kraken2	Kraken2 for taxonomic designation.						To update	http://ccb.jhu.edu/software/kraken/	Metagenomics	kraken2	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/	2.1.1	kraken2	2.1.3	(1/1)	(1/1)	(1/1)
+kraken2	185308.0	2367.0	kraken2	Kraken2 for taxonomic designation.	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/	2.1.1	kraken2	2.1.3	(1/1)	(1/1)	(1/1)
 samtools										To update	https://github.com/samtools/samtools	SAM		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools	1.15.1	samtools	1.19.2	(0/1)	(0/1)	(0/1)
 snpeff	101254.0	2843.0	snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names	SnpEff is a genetic variant annotation and effect prediction toolbox						To update	http://snpeff.sourceforge.net/	Genome-Wide Association Study, Variant Analysis	snpeff	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff		biopython	1.70	(5/5)	(5/5)	(5/5)
 snpsift	5109063.0	1185.0	snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck	snpEff SnpSift tools from Pablo Cingolani						To update	http://snpeff.sourceforge.net/SnpSift.html	Variant Analysis	snpsift	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift		snpsift	5.2	(8/8)	(8/8)	(8/8)
@@ -1149,7 +1151,7 @@ protxml_to_xls			protxml_to_xls							To update			protxml_to_xls	galaxyp		0.1.0
 psm_eval			psm_eval							To update			psm_eval	galaxyp		0.1.0	binaries_for_psm_eval		(0/1)	(0/1)	(0/1)
 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	1.0.3			(0/1)	(0/1)	(1/1)
 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	2.1.4	pyprophet	2.2.5	(0/6)	(4/6)	(6/6)
-pyteomics			mztab2tsv	Tools using the pyteomics library	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	4.4.1	pyteomics	4.6.3	(0/1)	(0/1)	(1/1)
+pyteomics			mztab2tsv	Tools using the pyteomics library	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	4.4.1	pyteomics	4.7	(0/1)	(0/1)	(1/1)
 quantp	230.0	6.0	quantp	Correlation between protein and transcript abundance						To update		Proteomics	quantp	galaxyp		1.1.2	r-data.table	1.11.6	(0/1)	(0/1)	(1/1)
 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	2.0	quantwiz-iq	2.0	(0/1)	(0/1)	(1/1)
 qupath_roi_splitter	59.0	5.0	qupath_roi_splitter	Split ROI coordinates of QuPath TMA annotation by cell type						To update	https://github.com/npinter/ROIsplitter	Imaging	qupath_roi_splitter	galaxyp	hhttps://github.com/npinter/ROIsplitter	0.1.0+galaxy1	geojson		(0/1)	(0/1)	(1/1)
@@ -1165,7 +1167,7 @@ uniprotxml_downloader	1360.0	79.0	uniprotxml_downloader	Download UniProt proteom
 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		0.1.5	validate-fasta-database	1.0	(0/1)	(0/1)	(1/1)
 bio3d			bio3d_dccm, bio3d_pca, bio3d_rmsd, bio3d_rmsf, bio3d_pca_visualize	Bio3d is a program that can be used to analyse molecular dynamics trajectories.						To update	http://thegrantlab.org/bio3d/index.php	Computational chemistry	bio3d	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/bio3d	2.4_1	r-bio3d	2.3_3	(5/5)	(4/5)	(5/5)
 biomoldyn			biomd_neqgamma, fastpca, biomd_extract_clusters, biomd_rmsd_clustering	Tools for MD analysis						To update	https://github.com/moldyn/	Molecular Dynamics, Computational chemistry	biomoldyn	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	1.5.2	scipy		(4/4)	(0/4)	(4/4)
-ambertools			ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap	Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.						To update	http://ambermd.org/AmberTools.php	Molecular Dynamics, Computational chemistry	ambertools	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	21.10	ambertools		(7/7)	(1/7)	(7/7)
+ambertools			ambertools_acpype, acpype_Amber2Gromacs, ambertools_antechamber, mmpbsa_mmgbsa, ambertools_parmchk2, parmconv, tleap	Ambertools is a set of packages for preparing systems for molecular dynamics (MD) simulations and analyzing trajectories.						To update	http://ambermd.org/AmberTools.php	Molecular Dynamics, Computational chemistry	ambertools	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/	21.10	ambertools		(7/7)	(2/7)	(7/7)
 packmol	288.0	15.0	packmol	PACKMOL is a package for creating starting structures for Molecular Dynamics simulations						To update	http://m3g.iqm.unicamp.br/packmol/home.shtml	Molecular Dynamics, Computational chemistry	packmol	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem	18.169.1	packmol		(1/1)	(0/1)	(1/1)
 topologyeditors			gromacs_modify_topology, gromacs_extract_topology	Set of python scripts and associated tool files that can be used to modify topology files.						To update	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	Molecular Dynamics, Computational chemistry	topologyeditors	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors	0	python		(2/2)	(0/2)	(2/2)
 free_energy				Free energy tools of BRIDGE.						To update		Molecular Dynamics, Computational chemistry	freeenergy	chemteam	https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy				(0/1)	(0/1)	(0/1)
@@ -1190,6 +1192,7 @@ concat_multi_datasets			cat_multi_datasets	Concatenate multiple datasets tail-to
 cpm_tpm_rpk			cpm_tpm_rpk	Generate CPM,TPM or RPK from raw counts						To update	http://artbio.fr	Transcriptomics	cpm_tpm_rpk	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/cpm_tpm_rpk	0.5.2	r-optparse	1.3.2	(0/1)	(0/1)	(0/1)
 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	1.40.2+galaxy0	bioconductor-deseq2	1.42.0	(0/1)	(0/1)	(0/1)
 embl2fa			embl2fa	Converts EMBL flat format to fasta format						To update	http://artbio.fr	Text Manipulation	embl2fa	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa	0.2			(0/1)	(0/1)	(0/1)
+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	3.4.4	r-ggplot2	2.2.1	(0/1)	(0/1)	(0/1)
 fetch_fasta_from_ncbi			retrieve_fasta_from_NCBI	Fetch fasta sequences from NCBI using eutils wrappers						To update	http://artbio.fr	Fasta Manipulation, Data Source	fetch_fasta_from_ncbi	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/fetch_fasta_from_ncbi	3.1.0	urllib3	1.12	(0/1)	(0/1)	(0/1)
 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	2.32.0+galaxy0	bioconductor-qvalue	2.34.0	(0/1)	(0/1)	(0/1)
 gatk4			filtermutectcalls, mergemutectstats, mutect2	Find somatic variations						To update	http://artbio.fr	Variant Analysis	gatk4	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4	4.1.7.0	gatk4	4.4.0.0	(0/3)	(0/3)	(0/3)
@@ -1207,10 +1210,10 @@ high_dim_heatmap			high_dim_heatmap	gplot heatmap.2 function adapted for plottin
 justdiff			justdiff	Unix diff						To update	http://artbio.fr	Text Manipulation	justdiff	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justdiff	3.10+galaxy0	diffutils		(0/1)	(0/1)	(0/1)
 justgzip			justgzip	Compress fastq sequence files						To update	http://artbio.fr	Convert Formats	justgzip	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/justgzip	2.8+galaxy0	pigz		(0/1)	(0/1)	(0/1)
 lumpy_smoove			lumpy_smoove, vcf2hrdetect	Galaxy wrapper of the lumpy-using smoove workflow						To update	http://artbio.fr	Variant Analysis	lumpy_smoove	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/lumpy_smoove	0.2.8+galaxy1	svtyper	0.7.1	(0/2)	(0/2)	(0/2)
-manta	93.0	8.0	manta	Structural variant and indel caller for mapped sequencing data						To update	http://artbio.fr	Variant Analysis	manta	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/manta	1.6	samtools	1.19.2	(0/1)	(0/1)	(1/1)
-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/master/tools/mapping_quality_stats	0.19.1+galaxy0	r-optparse	1.3.2	(0/1)	(0/1)	(0/1)
-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	1.5.1	tar		(0/1)	(1/1)	(0/1)
-mutational_patterns			mutational_patterns	Mutational patterns and signatures in base substitution catalogs						To update	http://artbio.fr	Variant Analysis	mutational_patterns	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns	3.4.0+galaxy2	bioconductor-mutationalpatterns	3.12.0	(0/1)	(0/1)	(0/1)
+manta	93.0	8.0	manta	Structural variant and indel caller for mapped sequencing data						To update	http://artbio.fr	Variant Analysis	manta	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/manta	1.6	samtools	1.19.2	(0/1)	(0/1)	(0/1)
+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	0.22.0	r-optparse	1.3.2	(0/1)	(0/1)	(0/1)
+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	1.6	tar		(0/1)	(1/1)	(0/1)
+mutational_patterns			mutational_patterns	Mutational patterns and signatures in base substitution catalogs						Up-to-date	http://artbio.fr	Variant Analysis	mutational_patterns	artbio	https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns	3.12.0	bioconductor-mutationalpatterns	3.12.0	(0/1)	(0/1)	(0/1)
 oases			oasesoptimiserv	Short read assembler						To update	http://artbio.fr	Assembly, RNA	oases	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/oases	1.3.0	oases	0.2.09	(0/1)	(0/1)	(0/1)
 pathifier	228.0	10.0	pathifier	pathifier						To update	https://	Transcriptomics, Statistics	pathifier	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/pathifier	1.0.2	r-optparse	1.3.2	(0/1)	(0/1)	(1/1)
 pindel			pindel	Pindel detects genome-wide structural variation.						To update	http://artbio.fr	Variant Analysis	pindel	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel	0.2.5b8+galaxy1	pindel	0.2.5b9	(0/1)	(0/1)	(0/1)
@@ -1249,7 +1252,7 @@ srs_tools			srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectr
 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	0.0.2			(0/5)	(0/5)	(5/5)
 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	0.1.1			(0/4)	(0/4)	(4/4)
 xmlstarlet	14.0	4.0	xmlstarlet	Tool to convert a xml file from one metadata standard to another						To update		Convert Formats	xmlstarlet	ecology	https://github.com/galaxyecology/tools-ecology/tree/main/tools-ecology/tools/xmlstarlet	1.6.1	xmlstarlet		(0/1)	(0/1)	(1/1)
-c3s	198.0	5.0	c3s	Copernicus Climate Change Service (C3S)						To update	https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset	Climate Analysis	c3s	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	0.1.0	python		(1/1)	(1/1)	(1/1)
+c3s	198.0	5.0	c3s	Copernicus Climate Change Service (C3S)						To update	https://cds.climate.copernicus.eu/cdsapp#!/search?type=dataset	Climate Analysis	c3s	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s	0.2.0	python		(1/1)	(1/1)	(1/1)
 cads	52.0	1.0	cads	Copernicus Atmosphere Data Store (ADS)						To update	https://ads.atmosphere.copernicus.eu/#!/home	Climate Analysis	cads	climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads	0.1.0	python		(0/1)	(0/1)	(1/1)
 cdo			cdo_info, cdo_operations	CDO (Climate Data Operators) is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.						To update	https://code.mpimet.mpg.de/projects/cdo/	Climate Analysis		climate	https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cdo	2.0.0			(0/2)	(0/2)	(2/2)
 cesm	13.0	1.0	cesm	Community Earth System Model (CESM)						Up-to-date	https://www.cesm.ucar.edu/	Climate Analysis	cesm	climate	https://github.com/ESCOMP/CESM	2.1.3	cesm	2.1.3	(0/1)	(0/1)	(1/1)
diff --git a/results/index.html b/results/index.html
index ab2b7a28..3348bdbd 100644
--- a/results/index.html
+++ b/results/index.html
@@ -1817,6 +1817,26 @@
       <td>workflow4metabolomics</td>
       <td>https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/genform/</td>
     </tr>
+    <tr>
+      <td></td>
+      <td>influx_data_manager</td>
+      <td>1.0.0</td>
+      <td>1.0.0</td>
+      <td>influx-si-data-manager</td>
+      <td>Up-to-date</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>Handling influx_si data inputs in Galaxy workflows</td>
+      <td></td>
+      <td>Up-to-date</td>
+      <td>https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/</td>
+      <td>Metabolomics</td>
+      <td>influx_si_data_manager</td>
+      <td>workflow4metabolomics</td>
+      <td>https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m/tree/main/tools/influx_data_manager</td>
+    </tr>
     <tr>
       <td></td>
       <td>influx_si</td>
@@ -3041,16 +3061,16 @@
       <td></td>
       <td>superdsm</td>
       <td>0.1.3</td>
-      <td>0.1.3</td>
+      <td>0.2.0</td>
       <td>superdsm</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>superdsm</td>
       <td>SuperDSM</td>
       <td>Image analysis</td>
       <td></td>
       <td>Globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images</td>
       <td>SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/bmcv</td>
       <td>Imaging</td>
       <td>superdsm</td>
@@ -5541,7 +5561,7 @@
       <td></td>
       <td>find_diag_hits</td>
       <td>1.0.0</td>
-      <td>0.9.0</td>
+      <td>0.10.0</td>
       <td>taxonomy</td>
       <td>To update</td>
       <td></td>
@@ -5561,7 +5581,7 @@
       <td></td>
       <td>gi2taxonomy</td>
       <td>1.1.1</td>
-      <td>0.9.0</td>
+      <td>0.10.0</td>
       <td>taxonomy</td>
       <td>To update</td>
       <td></td>
@@ -5601,7 +5621,7 @@
       <td></td>
       <td>lca_wrapper</td>
       <td>1.0.1</td>
-      <td>0.9.0</td>
+      <td>0.10.0</td>
       <td>taxonomy</td>
       <td>To update</td>
       <td></td>
@@ -5621,7 +5641,7 @@
       <td></td>
       <td>poisson2test</td>
       <td>1.0.0</td>
-      <td>0.9.0</td>
+      <td>0.10.0</td>
       <td>taxonomy</td>
       <td>To update</td>
       <td></td>
@@ -5641,7 +5661,7 @@
       <td></td>
       <td>t2ps</td>
       <td>1.0.0</td>
-      <td>0.9.0</td>
+      <td>0.10.0</td>
       <td>taxonomy</td>
       <td>To update</td>
       <td></td>
@@ -5661,7 +5681,7 @@
       <td></td>
       <td>t2t_report</td>
       <td>1.0.0</td>
-      <td>0.9.0</td>
+      <td>0.10.0</td>
       <td>taxonomy</td>
       <td>To update</td>
       <td></td>
@@ -9961,16 +9981,16 @@
       <td></td>
       <td>amrfinderplus</td>
       <td>3.11.26</td>
-      <td>3.11.26</td>
+      <td>3.12.8</td>
       <td>ncbi-amrfinderplus</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>amrfinderplus</td>
       <td>AMRFinderPlus</td>
       <td>Antimicrobial resistance prediction</td>
       <td>Microbiology, Public health and epidemiology, Infectious disease</td>
       <td>"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.</td>
       <td>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</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/ncbi/amr</td>
       <td>Sequence Analysis</td>
       <td>AMRFinderPlus</td>
@@ -10160,17 +10180,17 @@
     <tr>
       <td></td>
       <td>bakta</td>
-      <td>1.8.2</td>
+      <td>1.9.2</td>
       <td>1.9.2</td>
       <td>bakta</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>Bakta</td>
       <td>Bakta</td>
       <td>Genome annotation</td>
       <td>Genomics, Data submission, annotation and curation, Sequence analysis</td>
       <td>"Bakta is a tool for the rapid &amp; standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON &amp; bioinformatics standard file formats for automatic downstream analysis."</td>
       <td>Rapid &amp; standardized annotation of bacterial genomes, MAGs &amp; plasmids</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://github.com/oschwengers/bakta</td>
       <td>Sequence Analysis</td>
       <td>bakta</td>
@@ -10360,17 +10380,17 @@
     <tr>
       <td></td>
       <td>bbtools</td>
-      <td>39.01</td>
+      <td>39.06</td>
       <td>39.06</td>
       <td>bbmap</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td></td>
       <td></td>
       <td></td>
       <td></td>
       <td>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.</td>
       <td></td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>https://jgi.doe.gov/data-and-tools/bbtools/</td>
       <td>Sequence Analysis</td>
       <td>bbtools</td>
@@ -10604,12 +10624,12 @@
       <td>2.1.7</td>
       <td>biom-format</td>
       <td>To update</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>biomformat</td>
+      <td>biomformat</td>
+      <td>Formatting</td>
+      <td>Laboratory information management, Sequence analysis</td>
       <td>The biom-format package provides a command line interface and Python API for working with BIOM files.</td>
-      <td></td>
+      <td>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.</td>
       <td>To update</td>
       <td>https://github.com/biocore/biom-format</td>
       <td>Metagenomics</td>
@@ -10741,7 +10761,7 @@
       <td></td>
       <td>breseq</td>
       <td>0.35.5</td>
-      <td>0.38.2</td>
+      <td>0.38.3</td>
       <td>breseq</td>
       <td>To update</td>
       <td>breseq</td>
@@ -10837,6 +10857,26 @@
       <td>iuc</td>
       <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth</td>
     </tr>
+    <tr>
+      <td></td>
+      <td>cactus</td>
+      <td>2.7.1</td>
+      <td></td>
+      <td></td>
+      <td>To update</td>
+      <td>cactus</td>
+      <td>Cactus</td>
+      <td>Multiple sequence alignment, Genome alignment</td>
+      <td>Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics</td>
+      <td>Cactus is a reference-free whole-genome multiple alignment program</td>
+      <td>Cactus is a reference-free whole-genome multiple alignment program.</td>
+      <td>To update</td>
+      <td>https://github.com/ComparativeGenomicsToolkit/cactus</td>
+      <td>Sequence Analysis</td>
+      <td>cactus</td>
+      <td>galaxy-australia</td>
+      <td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus</td>
+    </tr>
     <tr>
       <td></td>
       <td>calculate_contrast_threshold</td>
@@ -10987,7 +11027,7 @@
       <td>cherri</td>
       <td>cherri</td>
       <td></td>
-      <td></td>
+      <td>Molecular interactions, pathways and networks, Structure analysis, Machine learning</td>
       <td>Computational Help Evaluating RNA-RNA interactions</td>
       <td>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.</td>
       <td>To update</td>
@@ -11184,12 +11224,12 @@
       <td>4.10.7</td>
       <td>paml</td>
       <td>To update</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>paml</td>
+      <td>PAML</td>
+      <td>Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis</td>
+      <td>Phylogenetics, Sequence analysis</td>
       <td>Detects positive selection</td>
-      <td></td>
+      <td>Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.</td>
       <td>To update</td>
       <td>http://abacus.gene.ucl.ac.uk/software/paml.html</td>
       <td>Phylogenetics</td>
@@ -11924,12 +11964,12 @@
       <td>1.4.6</td>
       <td>dram</td>
       <td>To update</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>dram</td>
+      <td>DRAM</td>
+      <td>Gene functional annotation</td>
+      <td>Metagenomics, Biological databases, Molecular genetics</td>
       <td>DRAM for distilling microbial metabolism to automate the curation of microbiome function</td>
-      <td></td>
+      <td>Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes</td>
       <td>To update</td>
       <td>https://github.com/WrightonLabCSU/DRAM</td>
       <td>Metagenomics</td>
@@ -12184,12 +12224,12 @@
       <td>0.22</td>
       <td>export2graphlan</td>
       <td>To update</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>export2graphlan</td>
+      <td>export2graphlan</td>
+      <td>Conversion</td>
+      <td>Taxonomy, Metabolomics, Biomarkers</td>
       <td>export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn</td>
-      <td></td>
+      <td>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.</td>
       <td>To update</td>
       <td>https://bitbucket.org/CibioCM/export2graphlan/overview</td>
       <td>Metagenomics</td>
@@ -12224,12 +12264,12 @@
       <td>0.1</td>
       <td>fargene</td>
       <td>Up-to-date</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>fargene</td>
+      <td>fARGene</td>
+      <td>Antimicrobial resistance prediction</td>
+      <td>Metagenomics, Microbiology, Public health and epidemiology</td>
       <td>fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )</td>
-      <td></td>
+      <td>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.</td>
       <td>Up-to-date</td>
       <td>https://github.com/fannyhb/fargene</td>
       <td>Sequence Analysis</td>
@@ -12344,14 +12384,14 @@
       <td>0.3.1</td>
       <td>fastqe</td>
       <td>To update</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>fastqe</td>
       <td>FASTQE</td>
-      <td></td>
+      <td>Sequencing quality control</td>
+      <td>Sequence analysis, Sequencing</td>
+      <td>FASTQE</td>
+      <td>Compute quality stats for FASTQ files and print those stats as emoji... for some reason.</td>
       <td>To update</td>
-      <td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe</td>
+      <td>https://fastqe.com/</td>
       <td>Sequence Analysis</td>
       <td>fastqe</td>
       <td>iuc</td>
@@ -12581,7 +12621,7 @@
       <td></td>
       <td>freyja</td>
       <td>1.4.4</td>
-      <td>1.4.8</td>
+      <td>1.4.9</td>
       <td>freyja</td>
       <td>To update</td>
       <td>freyja</td>
@@ -13124,14 +13164,14 @@
       <td>1.1.3</td>
       <td>graphlan</td>
       <td>To update</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>graphlan</td>
+      <td>GraPhlAn</td>
+      <td>Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification</td>
+      <td>Metagenomics, Phylogenetics, Phylogenomics, Cladistics</td>
       <td>GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees</td>
-      <td></td>
+      <td>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.</td>
       <td>To update</td>
-      <td>https://bitbucket.org/nsegata/graphlan/overview</td>
+      <td>https://github.com/biobakery/graphlan</td>
       <td>Metagenomics, Graphics, Phylogenetics</td>
       <td>graphlan</td>
       <td>iuc</td>
@@ -13144,12 +13184,12 @@
       <td>2.3.2</td>
       <td>gtdbtk</td>
       <td>To update</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>GTDB-Tk</td>
+      <td>GTDB-Tk</td>
+      <td>Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval</td>
+      <td>Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins</td>
       <td>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.</td>
-      <td></td>
+      <td>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).</td>
       <td>To update</td>
       <td>https://github.com/Ecogenomics/GTDBTk</td>
       <td>Metagenomics</td>
@@ -13244,12 +13284,12 @@
       <td>1.1.4</td>
       <td>hamronization</td>
       <td>To update</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>hamronization</td>
+      <td>hAMRonization</td>
+      <td>Data handling, Antimicrobial resistance prediction, Parsing</td>
+      <td>Public health and epidemiology, Microbiology, Bioinformatics</td>
       <td>Convert AMR gene detection tool output to hAMRonization specification format.</td>
-      <td></td>
+      <td>Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure</td>
       <td>To update</td>
       <td>https://github.com/pha4ge/hAMRonization</td>
       <td>Sequence Analysis</td>
@@ -13424,12 +13464,12 @@
       <td>hamtv0.3.1</td>
       <td>hifiasm_meta</td>
       <td>To update</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>hifiasm-meta</td>
+      <td>Hifiasm-meta</td>
+      <td>Sequence assembly</td>
+      <td>Sequence assembly, Metagenomics</td>
       <td>A hifiasm fork for metagenome assembly using Hifi reads.</td>
-      <td></td>
+      <td>Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.</td>
       <td>To update</td>
       <td>https://github.com/xfengnefx/hifiasm-meta</td>
       <td>Metagenomics</td>
@@ -13624,12 +13664,12 @@
       <td>1.3.1</td>
       <td>icescreen</td>
       <td>Up-to-date</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>icescreen</td>
+      <td>ICEscreen</td>
+      <td>Database search, Protein feature detection</td>
+      <td>Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation</td>
       <td>ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.</td>
-      <td></td>
+      <td>A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.</td>
       <td>Up-to-date</td>
       <td>https://icescreen.migale.inrae.fr/</td>
       <td>Genome annotation</td>
@@ -14021,7 +14061,7 @@
       <td></td>
       <td>jellyfish</td>
       <td></td>
-      <td>2.3.0</td>
+      <td>2.3.1</td>
       <td>kmer-jellyfish</td>
       <td>To update</td>
       <td>Jellyfish</td>
@@ -14321,7 +14361,7 @@
       <td></td>
       <td>last</td>
       <td>1205</td>
-      <td>1540</td>
+      <td>1541</td>
       <td>last</td>
       <td>To update</td>
       <td>last</td>
@@ -14420,17 +14460,17 @@
     <tr>
       <td></td>
       <td>limma_voom</td>
-      <td>3.50.1</td>
+      <td>3.58.1</td>
       <td>3.58.1</td>
       <td>bioconductor-limma</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>limma</td>
       <td>limma</td>
       <td>RNA-Seq analysis</td>
       <td>Molecular biology, Genetics</td>
       <td>Perform RNA-Seq differential expression analysis using limma voom pipeline</td>
       <td>Data analysis, linear models and differential expression for microarray data.</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://bioconductor.org/packages/release/bioc/html/limma.html</td>
       <td>Transcriptomics, RNA, Statistics</td>
       <td>limma_voom</td>
@@ -15761,7 +15801,7 @@
       <td></td>
       <td>novoplasty</td>
       <td>4.3.1</td>
-      <td>4.3.3</td>
+      <td>4.3.5</td>
       <td>novoplasty</td>
       <td>To update</td>
       <td></td>
@@ -16164,12 +16204,12 @@
       <td>1.46.0</td>
       <td>bioconductor-phyloseq</td>
       <td>To update</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>phyloseq</td>
+      <td>phyloseq</td>
+      <td>Deposition, Analysis, Visualisation</td>
+      <td>Microbiology, Sequence analysis, Metagenomics</td>
       <td>Handling and analysis of high-throughput microbiome census data</td>
-      <td></td>
+      <td>Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.</td>
       <td>To update</td>
       <td>https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html</td>
       <td>Metagenomics</td>
@@ -16244,12 +16284,12 @@
       <td>1.1.4</td>
       <td>picrust</td>
       <td>To update</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>picrust</td>
+      <td>PICRUSt</td>
+      <td>Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding</td>
+      <td>Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing</td>
       <td>PICRUSt wrappers</td>
-      <td></td>
+      <td>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.</td>
       <td>To update</td>
       <td>https://picrust.github.io/picrust/</td>
       <td>Metagenomics</td>
@@ -17061,16 +17101,16 @@
       <td></td>
       <td>recentrifuge</td>
       <td>1.13.2</td>
-      <td>1.13.2</td>
+      <td>1.14.0</td>
       <td>recentrifuge</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>Recentrifuge</td>
       <td>Recentrifuge</td>
       <td>Taxonomic classification, Expression analysis, Cross-assembly</td>
       <td>Metagenomics, Microbial ecology, Metagenomic sequencing</td>
       <td>"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."</td>
       <td>Robust comparative analysis and contamination removal for metagenomics.</td>
-      <td>Up-to-date</td>
+      <td>To update</td>
       <td>https://github.com/khyox/recentrifuge</td>
       <td>Metagenomics</td>
       <td>recentrifuge</td>
@@ -17220,7 +17260,7 @@
     <tr>
       <td></td>
       <td>rgrnastar</td>
-      <td>2.7.10b</td>
+      <td>2.7.11a</td>
       <td>2.7.11b</td>
       <td>star</td>
       <td>To update</td>
@@ -19561,7 +19601,7 @@
       <td></td>
       <td>verkko</td>
       <td>1.3.1</td>
-      <td>1.4.1</td>
+      <td>2.0</td>
       <td>verkko</td>
       <td>To update</td>
       <td></td>
@@ -20644,12 +20684,12 @@
       <td>2.1.3</td>
       <td>kraken2</td>
       <td>To update</td>
-      <td></td>
-      <td></td>
-      <td></td>
-      <td></td>
+      <td>kraken2</td>
+      <td>kraken2</td>
+      <td>Taxonomic classification</td>
+      <td>Taxonomy, Metagenomics</td>
       <td>Kraken2 for taxonomic designation.</td>
-      <td></td>
+      <td>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.</td>
       <td>To update</td>
       <td>http://ccb.jhu.edu/software/kraken/</td>
       <td>Metagenomics</td>
@@ -22801,7 +22841,7 @@
       <td></td>
       <td>pyteomics</td>
       <td>4.4.1</td>
-      <td>4.6.3</td>
+      <td>4.7</td>
       <td>pyteomics</td>
       <td>To update</td>
       <td>pyteomics</td>
@@ -23617,6 +23657,26 @@
       <td>artbio</td>
       <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/embl2fa</td>
     </tr>
+    <tr>
+      <td></td>
+      <td>ez_histograms</td>
+      <td>3.4.4</td>
+      <td>2.2.1</td>
+      <td>r-ggplot2</td>
+      <td>To update</td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td></td>
+      <td>ggplot2 histograms and density plots</td>
+      <td></td>
+      <td>To update</td>
+      <td>https://github.com/tidyverse/ggplot2</td>
+      <td>Visualization, Statistics</td>
+      <td>ez_histograms</td>
+      <td>artbio</td>
+      <td>https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms</td>
+    </tr>
     <tr>
       <td></td>
       <td>fetch_fasta_from_ncbi</td>
@@ -23980,7 +24040,7 @@
     <tr>
       <td></td>
       <td>mapping_quality_stats</td>
-      <td>0.19.1+galaxy0</td>
+      <td>0.22.0</td>
       <td>1.3.2</td>
       <td>r-optparse</td>
       <td>To update</td>
@@ -23995,12 +24055,12 @@
       <td>Sequence Analysis, Statistics</td>
       <td>mapping_quality_stats</td>
       <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/mapping_quality_stats</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/mapping_quality_stats</td>
     </tr>
     <tr>
       <td></td>
       <td>mircounts</td>
-      <td>1.5.1</td>
+      <td>1.6</td>
       <td></td>
       <td>tar</td>
       <td>To update</td>
@@ -24020,22 +24080,22 @@
     <tr>
       <td></td>
       <td>mutational_patterns</td>
-      <td>3.4.0+galaxy2</td>
+      <td>3.12.0</td>
       <td>3.12.0</td>
       <td>bioconductor-mutationalpatterns</td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td></td>
       <td></td>
       <td></td>
       <td></td>
       <td>Mutational patterns and signatures in base substitution catalogs</td>
       <td></td>
-      <td>To update</td>
+      <td>Up-to-date</td>
       <td>http://artbio.fr</td>
       <td>Variant Analysis</td>
       <td>mutational_patterns</td>
       <td>artbio</td>
-      <td>https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns</td>
+      <td>https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns</td>
     </tr>
     <tr>
       <td></td>
@@ -24800,7 +24860,7 @@
     <tr>
       <td></td>
       <td>c3s</td>
-      <td>0.1.0</td>
+      <td>0.2.0</td>
       <td></td>
       <td>python</td>
       <td>To update</td>