diff --git a/results/microgalaxy/index.html b/results/microgalaxy/index.html
index 77499dff..ce35e14d 100644
--- a/results/microgalaxy/index.html
+++ b/results/microgalaxy/index.html
@@ -811,35 +811,6 @@
(1/1) |
(0/1) |
-
- |
- ncbi_fcs_adaptor |
- |
- |
- ncbi_fcs_adaptor |
- FCS-adaptor detects adaptor and vector contamination in genome sequences. |
- |
- |
- |
- |
- |
- |
- |
- To update |
- https://github.com/ncbi/fcs |
- Sequence Analysis |
- ncbi_fcs_adaptor |
- richard-burhans |
- https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor |
- https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor |
- 0.5.0 |
- |
- |
- (1/1) |
- (0/1) |
- (0/1) |
- (0/1) |
-
|
suite_qiime2__alignment |
@@ -2261,35 +2232,6 @@
(0/1) |
(0/1) |
-
- |
- rbpbench |
- 36.0 |
- |
- rbpbench |
- Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs |
- rbpbench |
- rbpbench |
- |
- RBPBench |
- Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs |
- |
- RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis |
- Up-to-date |
- https://github.com/michauhl/RBPBench |
- Sequence Analysis, RNA, CLIP-seq |
- rbpbench |
- rnateam |
- https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench |
- https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench |
- 0.8.1 |
- rbpbench |
- 0.8.1 |
- (0/1) |
- (0/1) |
- (1/1) |
- (0/1) |
-
|
reago |
@@ -2377,35 +2319,6 @@
(3/3) |
(1/3) |
-
- |
- tapscan |
- |
- |
- tapscan_classify |
- Search for transcription associated proteins (TAPs) |
- |
- |
- |
- |
- |
- |
- |
- To update |
- https://plantcode.cup.uni-freiburg.de/tapscan/ |
- Proteomics |
- tapscan |
- bgruening |
- https://github.com/bgruening/galaxytools/tree/master/tools/tapscan |
- https://github.com/bgruening/galaxytools/tree/master/tools/tapscan |
- 4.76+galaxy0 |
- hmmer |
- 3.4 |
- (0/1) |
- (0/1) |
- (1/1) |
- (0/1) |
-
|
trim_galore |
@@ -3711,35 +3624,6 @@
(1/1) |
(1/1) |
-
- |
- cactus |
- |
- |
- cactus_cactus, cactus_export |
- Cactus is a reference-free whole-genome multiple alignment program |
- cactus |
- cactus |
- |
- Cactus |
- Cactus is a reference-free whole-genome multiple alignment program. |
- Multiple sequence alignment, Genome alignment |
- Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics |
- To update |
- https://github.com/ComparativeGenomicsToolkit/cactus |
- Sequence Analysis |
- cactus |
- galaxy-australia |
- https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus |
- https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus |
- 2.7.1 |
- |
- |
- (0/2) |
- (2/2) |
- (2/2) |
- (1/2) |
-
|
cat |
@@ -3972,35 +3856,6 @@
(3/3) |
(0/3) |
-
- |
- colabfold |
- |
- |
- colabfold_alphafold, colabfold_msa |
- Protein prediction based on AlphaFold2 |
- Colabfold |
- Colabfold |
- |
- ColabFold |
- ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. |
- Database search, Protein structure prediction, Fold recognition |
- Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics |
- To update |
- https://github.com/sokrypton/ColabFold |
- Proteomics, Graphics |
- colabfold |
- iuc |
- https://github.com/sokrypton/ColabFold |
- https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold |
- 1.5.5 |
- |
- |
- (2/2) |
- (0/2) |
- (0/2) |
- (0/2) |
-
|
compleasm |
@@ -5886,35 +5741,6 @@
(2/2) |
(2/2) |
-
- |
- mashmap |
- |
- |
- mashmap |
- Fast local alignment boundaries |
- |
- |
- |
- |
- |
- |
- |
- Up-to-date |
- https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap |
- Sequence Analysis |
- mashmap |
- iuc |
- https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap |
- https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap |
- 3.1.3 |
- mashmap |
- 3.1.3 |
- (0/1) |
- (0/1) |
- (1/1) |
- (0/1) |
-
|
maxbin2 |
@@ -6408,35 +6234,6 @@
(2/2) |
(2/2) |
-
- |
- mirmachine |
- |
- |
- mirmachine |
- Tool to detect miRNA in genome sequences |
- |
- |
- |
- |
- |
- |
- |
- Up-to-date |
- https://github.com/sinanugur/MirMachine |
- Sequence Analysis |
- mirmachine |
- iuc |
- https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine |
- https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine |
- 0.2.13 |
- mirmachine |
- 0.2.13 |
- (0/1) |
- (0/1) |
- (1/1) |
- (0/1) |
-
|
mitos |
@@ -6959,35 +6756,6 @@
(1/1) |
(1/1) |
-
- |
- pairtools |
- |
- |
- pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats |
- Flexible tools for Hi-C data processing |
- |
- |
- |
- |
- |
- |
- |
- Up-to-date |
- https://pairtools.readthedocs.io |
- Sequence Analysis |
- pairtools |
- iuc |
- https://github.com/open2c/pairtools |
- https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools |
- 1.1.0 |
- pairtools |
- 1.1.0 |
- (5/5) |
- (0/5) |
- (5/5) |
- (0/5) |
-
|
pharokka |
@@ -7191,6 +6959,35 @@
(1/1) |
(1/1) |
+
+ |
+ polypolish |
+ 239.0 |
+ 24.0 |
+ polypolish |
+ "Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix." |
+ Polypolish |
+ Polypolish |
+ |
+ Polypolish |
+ Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. |
+ Genome assembly, Read mapping, Mapping assembly, Sequencing error detection |
+ Sequence assembly, Sequence composition, complexity and repeats, Mapping |
+ To update |
+ https://github.com/rrwick/Polypolish |
+ Sequence Analysis |
+ polypolish |
+ iuc |
+ https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish |
+ https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish |
+ 0.5.0 |
+ polypolish |
+ 0.6.0 |
+ (0/1) |
+ (0/1) |
+ (1/1) |
+ (1/1) |
+
|
prodigal |
@@ -7597,35 +7394,6 @@
(1/1) |
(1/1) |
-
- |
- revoluzer |
- |
- |
- revoluzer_crex, revoluzer_distmat |
- revoluzer wrappers |
- revoluzer |
- revoluzer |
- |
- revoluzer |
- Various tools for genome rearrangement analysis. CREx, TreeREx, etc |
- Structural variation detection |
- Molecular evolution, Phylogeny |
- Up-to-date |
- https://gitlab.com/Bernt/revoluzer/ |
- Phylogenetics |
- revoluzer |
- iuc |
- https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer |
- https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer |
- 0.1.6 |
- revoluzer |
- 0.1.6 |
- (0/2) |
- (0/2) |
- (2/2) |
- (0/2) |
-
|
roary |
@@ -7887,6 +7655,35 @@
(1/1) |
(0/1) |
+
+ |
+ shorah |
+ |
+ |
+ shorah_amplicon |
+ Reconstruct haplotypes using ShoRAH in amplicon mode |
+ shorah |
+ shorah |
+ |
+ ShoRAH |
+ Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. |
+ Haplotype mapping, Variant calling |
+ Metagenomics, Sequencing, Genetics |
+ To update |
+ https://github.com/cbg-ethz/shorah/blob/master/README.md |
+ Sequence Analysis |
+ shorah_amplicon |
+ iuc |
+ https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah |
+ https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah |
+ 1.1.3 |
+ shorah |
+ 1.99.2 |
+ (0/1) |
+ (0/1) |
+ (0/1) |
+ (0/1) |
+
|
shovill |
@@ -8293,6 +8090,35 @@
(1/1) |
(0/1) |
+
+ |
+ 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 |
+ https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler |
+ 0.5.5 |
+ trycycler |
+ 0.5.5 |
+ (0/5) |
+ (5/5) |
+ (5/5) |
+ (5/5) |
+
|
unicycler |
@@ -8583,35 +8409,6 @@
(8/8) |
(8/8) |
-
- |
- windowmasker |
- 85.0 |
- |
- windowmasker_mkcounts, windowmasker_ustat |
- Identify repetitive regions using WindowMasker |
- |
- |
- |
- |
- |
- |
- |
- To update |
- https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ |
- Sequence Analysis |
- windowmasker |
- iuc |
- https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ |
- https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker |
- 1.0 |
- blast |
- 2.15.0 |
- (0/2) |
- (2/2) |
- (2/2) |
- (0/2) |
-
|
bamtools |
@@ -9830,35 +9627,6 @@
(0/1) |
(0/1) |
-
- |
- Geom_mean_workflow |
- |
- |
- Map_shp, Mean_geom, bar_plot |
- Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). |
- |
- |
- |
- |
- |
- |
- |
- To update |
- https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom |
- Ecology |
- Geometric means (Dead wood) |
- ecology |
- https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow |
- https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow |
- 0.1.0+galaxy0 |
- r-base |
- |
- (0/3) |
- (0/3) |
- (3/3) |
- (3/3) |
-
|
PAMPA |
@@ -9888,64 +9656,6 @@
(5/5) |
(5/5) |
-
- |
- interpolation |
- |
- |
- interpolation_run_idw_interpolation |
- Run IDW interpolation based on a .csv and .geojson file |
- |
- |
- |
- |
- |
- |
- |
- To update |
- https://github.com/AquaINFRA/galaxy |
- Ecology |
- |
- ecology |
- https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation |
- https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation |
- 1.0 |
- r-getopt |
- |
- (0/1) |
- (0/1) |
- (1/1) |
- (0/1) |
-
-
- |
- medenv |
- |
- |
- iabiodiv_smartbiodiv_med_environ |
- Retrieve environmental data from etopo, cmems and woa |
- |
- |
- |
- |
- |
- |
- |
- To update |
- https://github.com/jeremyfix/medenv |
- Ecology, Data Source |
- |
- ecology |
- https://github.com/jeremyfix/medenv |
- https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv |
- 0.1.0 |
- pandas |
- |
- (0/1) |
- (0/1) |
- (1/1) |
- (0/1) |
-
|
obisindicators |
@@ -9975,122 +9685,6 @@
(2/2) |
(1/2) |
-
- |
- ocean |
- |
- |
- argo_getdata |
- Access, process, visualise oceanographic data for the Earth System |
- |
- |
- |
- |
- |
- |
- |
- To update |
- https://github.com/Marie59/FE-ft-ESG/tree/main/argo |
- Ecology |
- |
- ecology |
- https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean |
- https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean |
- 0.1.15 |
- |
- |
- (0/1) |
- (0/1) |
- (1/1) |
- (0/1) |
-
-
- |
- ogcProcess_otb_bandmath |
- |
- |
- otb_band_math |
- Outputs a monoband image which is the result of a mathematical operation on several multi-band images. |
- |
- |
- |
- |
- |
- |
- |
- To update |
- https://github.com/AquaINFRA/galaxy |
- Ecology |
- |
- ecology |
- https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath |
- https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath |
- 1.0 |
- r-base |
- |
- (0/1) |
- (0/1) |
- (1/1) |
- (0/1) |
-
-
- |
- ogcProcess_otb_meanShiftSmoothing |
- |
- |
- otb_mean_shift_smoothing |
- This application smooths an image using the MeanShift algorithm. |
- |
- |
- |
- |
- |
- |
- |
- To update |
- https://github.com/AquaINFRA/galaxy |
- Ecology |
- |
- ecology |
- https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation |
- https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing |
- 1.0 |
- r-base |
- |
- (0/1) |
- (0/1) |
- (1/1) |
- (0/1) |
-
-
- |
- sdmpredictors |
- |
- |
- sdmpredictors_list_layers |
- Terrestrial and marine predictors for species distribution modelling. |
- |
- |
- |
- |
- |
- |
- |
- To update |
- https://cran.r-project.org/web/packages/sdmpredictors/index.html |
- Ecology |
- sdmpredictors |
- ecology |
- https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors |
- https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors |
- 0.2.15 |
- r-base |
- |
- (0/1) |
- (0/1) |
- (0/1) |
- (0/1) |
-
|
zoo_project_ogc_api_processes |
diff --git a/results/microgalaxy/tools.tsv b/results/microgalaxy/tools.tsv
index 1f6ef416..7176845d 100644
--- a/results/microgalaxy/tools.tsv
+++ b/results/microgalaxy/tools.tsv
@@ -59,31 +59,31 @@ stringmlst stringmlst Rapid and accurate identification of the sequence type (
wade wade identify regions of interest To update https://github.com/phac-nml/wade Sequence Analysis wade nml https://github.com/phac-nml/wade https://github.com/phac-nml/galaxy_tools/tree/master/tools/wade 0.2.5+galaxy1 wade 0.2.6 (0/1) (0/1) (0/1) (0/1) True False
isoplot 2.0 1.0 isoplot Isoplot is a software for the visualisation of MS data from C13 labelling experiments To update Metabolomics, Visualization isoplot workflow4metabolomics https://github.com/llegregam/Isoplot/tree/main https://github.com/workflow4metabolomics/tools-metabolomics/tree/master/tools/isoplot 1.3.0+galaxy1 isoplot 1.3.1 (0/1) (0/1) (1/1) (1/1) True False
repeatexplorer2 repeatexplorer_clustering Tool for annotation of repeats from unassembled shotgun reads. To update https://github.com/repeatexplorer/repex_tarean Genome annotation repeatexplorer2 gga https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/repeatexplorer2 2.3.8 (0/1) (0/1) (1/1) (0/1) True True
-ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. To update https://github.com/ncbi/fcs Sequence Analysis ncbi_fcs_adaptor richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 0.5.0 (1/1) (0/1) (0/1) (0/1) False
-suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) False
-suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) False
-suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) False
-suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) False
-suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.2.0+q2galaxy.2024.2.1 (21/22) (21/22) (21/22) (21/22) False
-suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) False
-suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.2.0+q2galaxy.2024.2.1 (10/11) (10/11) (10/11) (10/11) False
-suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.2.2+q2galaxy.2024.2.1 (17/22) (17/22) (17/22) (17/22) False
-suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) False
-suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) False
-suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) False
-suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) False
-suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) False
+ncbi_fcs_adaptor ncbi_fcs_adaptor FCS-adaptor detects adaptor and vector contamination in genome sequences. To update https://github.com/ncbi/fcs Sequence Analysis ncbi_fcs_adaptor richard-burhans https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_fcs_adaptor 0.5.0 (1/1) (0/1) (0/1) (0/1) True False
+suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True True
+suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) True True
+suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True True
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+suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True True
+suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) True True
+suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.2.0+q2galaxy.2024.2.1 (21/22) (21/22) (21/22) (21/22) True True
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+suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True True
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+suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.2.2+q2galaxy.2024.2.1 (17/22) (17/22) (17/22) (17/22) True True
+suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True True
+suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) True True
+suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) True True
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+suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) True True
+suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) True True
suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) False
-suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) False
-suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) False
-suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) False
-suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) False
-suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) False
-frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) False
+suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) True True
+suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True True
+suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) True True
+suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) True True
+suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) True True
+frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) True True
best_regression_subsets 3.0 BestSubsetsRegression1 Perform Best-subsets Regression To update Sequence Analysis, Variant Analysis best_regression_subsets devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/best_regression_subsets https://github.com/galaxyproject/tools-devteam/tree/main/tools/best_regression_subsets 1.0.0 numpy (1/1) (0/1) (1/1) (1/1) True False
blat_coverage_report generate_coverage_report Polymorphism of the Reads To update Next Gen Mappers, Sequence Analysis blat_coverage_report devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_coverage_report https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_coverage_report 1.0.0 (0/1) (0/1) (0/1) (0/1) True False
blat_mapping blat2wig Coverage of the Reads in wiggle format To update Next Gen Mappers, Sequence Analysis blat_mapping devteam https://github.com/galaxyproject/tools-devteam/tree/master/tools/blat_mapping https://github.com/galaxyproject/tools-devteam/tree/main/tools/blat_mapping 1.0.0 (0/1) (0/1) (0/1) (0/1) True False
@@ -220,7 +220,7 @@ nastiseq 40.0 nastiseq A method to identify cis-NATs using ssRNA-seq Up-
paralyzer 299.0 7.0 paralyzer A method to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. Up-to-date https://ohlerlab.mdc-berlin.de/software/PARalyzer_85/ RNA paralyzer rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer 1.5 paralyzer 1.5 (0/1) (0/1) (1/1) (0/1) True False
pipmir 275.0 21.0 pipmir A method to identify novel plant miRNA. To update https://ohlerlab.mdc-berlin.de/software/Pipeline_for_the_Identification_of_Plant_miRNAs_84/ RNA pipmir rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir 0.1.0 pipmir 1.1 (0/1) (0/1) (1/1) (0/1) True False
rRNA meta_rna Identification of ribosomal RNA genes in metagenomic fragments. To update http://weizhong-lab.ucsd.edu/meta_rna/ RNA rrna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rRNA https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rRNA 0.1 hmmsearch3.0 (0/1) (0/1) (0/1) (0/1) True True
-rbpbench 36.0 rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs rbpbench rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis Up-to-date https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench 0.8.1 rbpbench 0.8.1 (0/1) (0/1) (1/1) (0/1) False
+rbpbench 36.0 rbpbench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs rbpbench rbpbench RBPBench Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs RNA, Protein interactions, RNA immunoprecipitation, Bioinformatics, Sequence analysis Up-to-date https://github.com/michauhl/RBPBench Sequence Analysis, RNA, CLIP-seq rbpbench rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rbpbench 0.8.1 rbpbench 0.8.1 (0/1) (0/1) (1/1) (0/1) True False
rcas 1226.0 38.0 rcas RCAS (RNA Centric Annotation System) for functional analysis of transcriptome-wide regions detected by high-throughput experiments To update https://github.com/BIMSBbioinfo/RCAS RNA rcas rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas 1.5.4 bioconductor-rcas 1.28.2 (0/1) (0/1) (1/1) (0/1) True False
reago reago Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data. reago reago REAGO This is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. Sequence assembly Sequence assembly, RNA, Metagenomics, Microbiology Up-to-date https://github.com/chengyuan/reago-1.1 Metagenomics, RNA reago rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago 1.1 reago 1.1 (0/1) (0/1) (1/1) (0/1) True True
remurna 42.0 2.0 remurna remuRNA - Measurement of Single Nucleotide Polymorphism induced Changes of RNA Conformation To update https://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/index.cgi#remurna RNA remurna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/remurna 1.0.0 remurna 1.0 (0/1) (0/1) (1/1) (0/1) True False
@@ -240,7 +240,7 @@ trna_prediction 2935.0 236.0 aragorn_trna, trnascan Aragorn predicts tRNA and tm
vienna_rna 799.0 viennarna_kinfold, viennarna_kinwalker, viennarna_rna2dfold, viennarna_rnaaliduplex, viennarna_rnaalifold, viennarna_rnacofold, viennarna_rnadistance, viennarna_rnaduplex, viennarna_rnaeval, viennarna_rnafold, viennarna_rnaheat, viennarna_rnainverse, viennarna_rnalalifold, viennarna_rnalfold, viennarna_rnapaln, viennarna_rnadpdist, viennarna_rnapkplex, viennarna_rnaplex, viennarna_rnaplfold, viennarna_rnaplot, viennarna_rnasnoop, viennarna_rnasubopt, viennarna_rnaup ViennaRNA - Prediction and comparison of RNA secondary structures To update http://www.tbi.univie.ac.at/RNA/ RNA viennarna rnateam https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/vienna_rna 2.2.10 viennarna 2.6.4 (0/23) (0/23) (21/23) (0/23) True False
sailfish 4024.0 55.0 sailfish Sailfish is a tool for transcript quantification from RNA-seq data To update http://www.cs.cmu.edu/~ckingsf/software/sailfish/ Sequence Analysis, RNA sailfish bgruening https://github.com/bgruening/galaxytools/tree/master/tools/sailfish https://github.com/bgruening/galaxytools/tree/master/tools/sailfish 0.10.1.1 bzip2 (1/1) (1/1) (1/1) (1/1) True False
salmon 55161.0 746.0 alevin, salmon, salmonquantmerge Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq and single-cell data. salmon salmon Salmon A tool for transcript expression quantification from RNA-seq data Sequence composition calculation, RNA-Seq quantification, Gene expression analysis RNA-Seq, Gene expression, Transcriptomics To update https://github.com/COMBINE-lab/salmon Sequence Analysis, RNA, Transcriptomics bgruening https://github.com/bgruening/galaxytools/tree/master/tools/salmon https://github.com/bgruening/galaxytools/tree/master/tools/salmon 1.10.1 salmon 1.10.3 (2/3) (1/3) (3/3) (1/3) True True
-tapscan tapscan_classify Search for transcription associated proteins (TAPs) To update https://plantcode.cup.uni-freiburg.de/tapscan/ Proteomics tapscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tapscan https://github.com/bgruening/galaxytools/tree/master/tools/tapscan 4.76+galaxy0 hmmer 3.4 (0/1) (0/1) (1/1) (0/1) False
+tapscan tapscan_classify Search for transcription associated proteins (TAPs) To update https://plantcode.cup.uni-freiburg.de/tapscan/ Proteomics tapscan bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tapscan https://github.com/bgruening/galaxytools/tree/master/tools/tapscan 4.76+galaxy0 hmmer 3.4 (0/1) (0/1) (1/1) (0/1) True False
tgsgapcloser 460.0 36.0 tgsgapcloser TGS-GapCloser uses error-prone long reads or preassembled contigs to fill N-gap in the genome assembly. TGS-GapCloser TGS-GapCloser TGS-GapCloser TGS-GapCloser is a fast and accurately passing through the Bermuda in large genome using error-prone third-generation long reads. Genome assembly, Read mapping, Scaffolding, Localised reassembly Sequencing, Sequence assembly, Phylogeny, Transcription factors and regulatory sites, Mapping To update https://github.com/BGI-Qingdao/TGS-GapCloser Assembly tgsgapcloser bgruening https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser https://github.com/bgruening/galaxytools/tree/master/tools/tgsgapcloser 1.0.3 tgsgapcloser 1.2.1 (0/1) (0/1) (1/1) (0/1) True False
trim_galore 238699.0 2334.0 trim_galore Trim Galore adaptive quality and adapter trimmer trim_galore trim_galore Trim Galore A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. Sequence trimming, Primer removal, Read pre-processing Sequence analysis To update http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Sequence Analysis, Fastq Manipulation trim_galore bgruening https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore 0.6.7 trim-galore 0.6.10 (1/1) (1/1) (1/1) (1/1) True True
uniprot_rest_interface 2406.0 132.0 uniprot UniProt ID mapping and sequence retrieval To update https://github.com/jdrudolph/uniprot Proteomics, Sequence Analysis uniprot_rest_interface bgruening https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface 0.4 requests (1/1) (1/1) (1/1) (0/1) True False
@@ -274,30 +274,30 @@ seq_primer_clip seq_primer_clip Trim off 5' or 3' primers To update htt
seq_rename seq_rename Rename sequences with ID mapping from a tabular file To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename Fasta Manipulation, Sequence Analysis, Text Manipulation seq_rename peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_rename 0.0.10 galaxy_sequence_utils 1.1.5 (0/1) (0/1) (0/1) (0/1) True False
seq_select_by_id seq_select_by_id Select sequences by ID To update https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id Fasta Manipulation, Sequence Analysis, Text Manipulation seq_select_by_id peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id 0.0.15 biopython 1.70 (0/1) (1/1) (0/1) (0/1) True False
venn_list 5067.0 248.0 venn_list Draw Venn Diagram (PDF) from lists, FASTA files, etc To update https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list Graphics, Sequence Analysis, Visualization venn_list peterjc https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list 0.1.2 galaxy_sequence_utils 1.1.5 (1/1) (0/1) (1/1) (1/1) True False
-suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) False
-suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) False
-suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) False
-suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) False
-suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.2.0+q2galaxy.2024.2.1 (21/22) (21/22) (21/22) (21/22) False
-suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) False
-suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.2.0+q2galaxy.2024.2.1 (10/11) (10/11) (10/11) (10/11) False
-suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.2.2+q2galaxy.2024.2.1 (17/22) (17/22) (17/22) (17/22) False
-suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) False
-suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) False
-suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) False
-suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) False
-suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) False
+suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True True
+suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) True True
+suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True True
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+suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True True
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+suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True True
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+suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) True True
+suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) True True
+suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) True True
+suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) True True
suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) False
-suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) False
-suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) False
-suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) False
-suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) False
-suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) False
-frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) False
+suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) True True
+suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True True
+suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) True True
+suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) True True
+suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) True True
+frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) True True
TrimNs trimns TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline To update https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs Assembly trimns iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimN https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs 0.1.0 trimns_vgp 1.0 (0/1) (0/1) (1/1) (0/1) True False
abricate 496717.0 1764.0 abricate, abricate_list, abricate_summary Mass screening of contigs for antiobiotic resistance genes ABRicate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. Antimicrobial resistance prediction Genomics, Microbiology Up-to-date https://github.com/tseemann/abricate Sequence Analysis abricate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate 1.0.1 abricate 1.0.1 (3/3) (3/3) (3/3) (3/3) True True
abritamr abritamr A pipeline for running AMRfinderPlus and collating results into functional classes abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease To update https://zenodo.org/record/7370628 Sequence Analysis abritamr iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr 1.0.14 abritamr 1.0.17 (0/1) (0/1) (1/1) (0/1) True True
@@ -337,7 +337,7 @@ blastxml_to_gapped_gff3 185.0 24.0 blastxml_to_gapped_gff3 BlastXML to gapped GF
bracken 18351.0 326.0 est_abundance Bayesian Reestimation of Abundance with KrakEN bracken bracken Bracken Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Statistical calculation Metagenomics, Microbial ecology Up-to-date https://ccb.jhu.edu/software/bracken/ Sequence Analysis, Metagenomics bracken iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken 2.9 bracken 2.9 (1/1) (1/1) (1/1) (1/1) True True
busco 86180.0 1804.0 busco BUSCO assess genome and annotation completeness busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis To update https://gitlab.com/ezlab/busco/-/releases Sequence Analysis busco iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco 5.5.0 busco 5.7.1 (1/1) (1/1) (1/1) (1/1) True True
bwameth 10619.0 201.0 bwameth Fast and accurate alignment of BS-seq reads To update https://github.com/brentp/bwa-meth Sequence Analysis, Next Gen Mappers bwameth iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwameth https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth 0.2.6 bwameth 0.2.7 (1/1) (1/1) (1/1) (0/1) True False
-cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics To update https://github.com/ComparativeGenomicsToolkit/cactus Sequence Analysis cactus galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus 2.7.1 (0/2) (2/2) (2/2) (1/2) False
+cactus cactus_cactus, cactus_export Cactus is a reference-free whole-genome multiple alignment program cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics To update https://github.com/ComparativeGenomicsToolkit/cactus Sequence Analysis cactus galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus 2.7.1 (0/2) (2/2) (2/2) (1/2) True False
calculate_contrast_threshold calculate_contrast_threshold Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. To update https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold Visualization, Genomic Interval Operations, SAM calculate_contrast_threshold iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/calculate_contrast_threshold https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold 1.0.0 numpy (0/1) (0/1) (0/1) (0/1) True False
cat cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise Contig Annotation Tool (CAT) cat_bins cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly To update https://github.com/dutilh/CAT Metagenomics contig_annotation_tool iuc https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat 5.2.3 cat 5.3 (5/5) (2/5) (5/5) (0/5) True True
cdhit 8278.0 6.0 cd_hit Cluster or compare biological sequence datasets cd-hit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. Sequence clustering Sequencing Up-to-date http://weizhongli-lab.org/cd-hit/ Sequence Analysis, Fasta Manipulation cd_hit iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cdhit https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit 4.8.1 cd-hit 4.8.1 (0/1) (0/1) (1/1) (1/1) True True
@@ -352,7 +352,7 @@ clair3 1856.0 68.0 clair3 Symphonizing pileup and full-alignment for high-perfor
clustalw 46793.0 651.0 clustalw ClustalW multiple sequence alignment program for DNA or proteins clustal2 clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. Multiple sequence alignment Phylogeny, Sequence analysis Up-to-date http://www.clustal.org/clustal2/ Phylogenetics, Sequence Analysis clustalw devteam https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustalw https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw 2.1 clustalw 2.1 (1/1) (1/1) (1/1) (1/1) True True
codeml 60901.0 29.0 codeml Detects positive selection paml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Phylogenetics, Sequence analysis To update http://abacus.gene.ucl.ac.uk/software/paml.html Phylogenetics codeml iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml 4.9 paml 4.10.7 (0/1) (0/1) (1/1) (0/1) True True
cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut co-occurrence of mutations on amplicons cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. Genetic variation Up-to-date https://github.com/cbg-ethz/cojac Metagenomics, Sequence Analysis cojac iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac 0.9.1 cojac 0.9.1 (2/3) (0/3) (3/3) (0/3) True True
-colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 Colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics To update https://github.com/sokrypton/ColabFold Proteomics, Graphics colabfold iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold 1.5.5 (2/2) (0/2) (0/2) (0/2) False
+colabfold colabfold_alphafold, colabfold_msa Protein prediction based on AlphaFold2 Colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics To update https://github.com/sokrypton/ColabFold Proteomics, Graphics colabfold iuc https://github.com/sokrypton/ColabFold https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold 1.5.5 (2/2) (0/2) (0/2) (0/2) True False
colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome To update https://colibread.inria.fr/ Sequence Analysis, Variant Analysis colibread iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread 24.7.14+galaxy0 commet 24.7.14 (0/7) (0/7) (1/7) (1/7) True False
compleasm compleasm Compleasm: a faster and more accurate reimplementation of BUSCO compleasm compleasm compleasm """Compleasm: a faster and more accurate reimplementation of BUSCO""" Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly Sequence assembly, Genomics, Transcriptomics, Sequence analysis Up-to-date https://github.com/huangnengCSU/compleasm Sequence Analysis compleasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm 0.2.6 compleasm 0.2.6 (0/1) (0/1) (1/1) (1/1) True True
concoct 250.0 29.0 concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Sequence clustering, Read binning Metagenomics Up-to-date https://github.com/BinPro/CONCOCT Metagenomics concoct iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct 1.1.0 concoct 1.1.0 (0/5) (0/5) (5/5) (5/5) True True
@@ -462,7 +462,7 @@ macs2 84202.0 1968.0 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgp
maker 4950.0 419.0 maker, maker_map_ids MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. Genome annotation Genomics, DNA, Sequence analysis To update http://www.yandell-lab.org/software/maker.html Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker 2.31.11 maker 3.01.03 (2/2) (2/2) (2/2) (2/2) True True
mapseq 167.0 2.0 mapseq fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs To update https://github.com/jfmrod/MAPseq Metagenomics mapseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq 2.1.1 perl (0/1) (0/1) (1/1) (0/1) True True
mash 1739.0 12.0 mash_screen, mash_sketch Fast genome and metagenome distance estimation using MinHash mash mash Mash Fast genome and metagenome distance estimation using MinHash. Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Up-to-date https://github.com/marbl/Mash Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash 2.3 mash 2.3 (2/2) (2/2) (2/2) (2/2) True True
-mashmap mashmap Fast local alignment boundaries Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap Sequence Analysis mashmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap 3.1.3 mashmap 3.1.3 (0/1) (0/1) (1/1) (0/1) False
+mashmap mashmap Fast local alignment boundaries Up-to-date https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap Sequence Analysis mashmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap 3.1.3 mashmap 3.1.3 (0/1) (0/1) (1/1) (0/1) True False
masigpro 576.0 13.0 masigpro Identify significantly differential expression profiles in time-course microarray experiments masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq To update https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html Transcriptomics, RNA, Statistics masigpro iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro 1.49.3 coreutils 8.25 (1/1) (0/1) (1/1) (0/1) True False
maxbin2 2059.0 118.0 maxbin2 clusters metagenomic contigs into bins maxbin maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Sequence assembly Metagenomics, Sequence assembly, Microbiology To update https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html Metagenomics maxbin2 mbernt https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 maxbin2 2.2.7 (1/1) (1/1) (1/1) (1/1) True True
mcl 29.0 10.0 mcl The Markov Cluster Algorithm, a cluster algorithm for graphs mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. Clustering, Network analysis, Gene regulatory network analysis Molecular interactions, pathways and networks Up-to-date https://micans.org/mcl/man/mcl.html Sequence Analysis mcl iuc https://github.com/galaxyproject/tools-iuc/tree/master/mcl https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl 22.282 mcl 22.282 (0/1) (0/1) (1/1) (0/1) True True
@@ -477,12 +477,12 @@ metabat2 4072.0 154.0 metabat2_jgi_summarize_bam_contig_depths, metabat2 MetaBAT
metaeuk metaeuk_easy_predict MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. MetaEuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics Homology-based gene prediction Metagenomics, Gene and protein families To update https://github.com/soedinglab/metaeuk Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk 5.34c21f2 metaeuk 6.a5d39d9 (0/1) (0/1) (1/1) (0/1) True True
metagenomeseq metagenomeseq_normalizaton metagenomeSeq Normalization metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. Sequence visualisation, Statistical calculation Metagenomics, Sequencing To update Metagenomics metagenomeseq_normalization iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metagenomeseq https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq 1.16.0-0.0.1 bioconductor-metagenomeseq 1.43.0 (1/1) (0/1) (1/1) (1/1) True True
metaphlan 10507.0 427.0 customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan MetaPhlAn for Metagenomic Phylogenetic Analysis metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. Nucleic acid sequence analysis, Phylogenetic tree analysis Metagenomics, Phylogenomics To update https://github.com/biobakery/MetaPhlAn Metagenomics metaphlan iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan 4.0.6 metaphlan 4.1.0 (1/4) (2/4) (4/4) (4/4) True True
-metawrapmg metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis metawrap metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Up-to-date https://github.com/bxlab/metaWRAP Metagenomics metawrapmg_binning galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg 1.3.0 metawrap-mg 1.3.0 (0/1) (1/1) (1/1) (0/1) False
+metawrapmg metawrapmg_binning A flexible pipeline for genome-resolved metagenomic data analysis metawrap metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Up-to-date https://github.com/bxlab/metaWRAP Metagenomics metawrapmg_binning galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/master/tools/metawrapmg https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg 1.3.0 metawrap-mg 1.3.0 (0/1) (1/1) (1/1) (0/1) True True
migmap 1226.0 7.0 migmap mapper for full-length T- and B-cell repertoire sequencing MiGMAP MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Up-to-date https://github.com/mikessh/migmap RNA, Sequence Analysis migmap iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/migmap https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap 1.0.3 migmap 1.0.3 (1/1) (0/1) (1/1) (0/1) True False
minia 2206.0 109.0 minia Short-read assembler based on a de Bruijn graph minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Genome assembly Sequence assembly Up-to-date https://gatb.inria.fr/software/minia/ Assembly minia iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia 3.2.6 minia 3.2.6 (0/1) (1/1) (1/1) (0/1) True True
miniasm 11938.0 178.0 miniasm Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. De-novo assembly Genomics, Sequence assembly To update https://github.com/lh3/miniasm Assembly miniasm iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniasm https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm 0.3_r179 miniasm 0.3 (1/1) (1/1) (1/1) (1/1) True True
miniprot 813.0 15.0 miniprot, miniprot_index Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Up-to-date https://github.com/lh3/miniprot Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot 0.13 miniprot 0.13 (0/2) (0/2) (2/2) (2/2) True True
-mirmachine mirmachine Tool to detect miRNA in genome sequences Up-to-date https://github.com/sinanugur/MirMachine Sequence Analysis mirmachine iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0.2.13 mirmachine 0.2.13 (0/1) (0/1) (1/1) (0/1) False
+mirmachine mirmachine Tool to detect miRNA in genome sequences Up-to-date https://github.com/sinanugur/MirMachine Sequence Analysis mirmachine iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine 0.2.13 mirmachine 0.2.13 (0/1) (0/1) (1/1) (0/1) True False
mirnature 10.0 4.0 mirnature Computational detection of canonical microRNAs Up-to-date https://github.com/Bierinformatik/miRNAture RNA, Sequence Analysis mirnature iuc https://github.com/Bierinformatik/miRNAture https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature 1.1 mirnature 1.1 (0/1) (0/1) (1/1) (0/1) True False
mitobim 881.0 66.0 mitobim assemble mitochondrial genomes Up-to-date https://github.com/chrishah/MITObim Assembly mitobim iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitobim https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim 1.9.1 mitobim 1.9.1 (0/1) (1/1) (1/1) (0/1) True False
mitos 32022.0 58.0 mitos, mitos2 de-novo annotation of metazoan mitochondrial genomes mitos mitos MITOS De novo metazoan mitochondrial genome annotation. Genome annotation Zoology, Whole genome sequencing To update http://mitos.bioinf.uni-leipzig.de/ Sequence Analysis mitos iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos 1.1.7 mitos 2.1.9 (1/2) (1/2) (2/2) (0/2) True True
@@ -496,7 +496,7 @@ naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_
nanocompore nanocompore_db, nanocompore_sampcomp Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. Nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites To update https://nanocompore.rna.rocks/ Sequence Analysis nanocompore iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore 1.0.0rc3.post2 nanocompore 1.0.4 (0/2) (1/2) (2/2) (0/2) True True
nanoplot 63235.0 2195.0 nanoplot Plotting tool for long read sequencing data and alignments nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences Scatter plot plotting, Box-Whisker plot plotting Genomics Up-to-date https://github.com/wdecoster/NanoPlot Visualization nanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot 1.42.0 nanoplot 1.42.0 (1/1) (1/1) (1/1) (1/1) True True
nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation To update https://a-slide.github.io/NanopolishComp Sequence Analysis nanopolishcomp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanopolishcomp https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp 0.6.11 nanopolishcomp 0.6.12 (0/2) (0/2) (2/2) (2/2) True True
-ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.0 ncbi-fcs-gx 0.5.0 (1/1) (0/1) (1/1) (0/1) False
+ncbi_fcs_gx ncbi_fcs_gx FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). Up-to-date https://github.com/ncbi/fcs-gx Sequence Analysis ncbi_fcs_gx iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx 0.5.0 ncbi-fcs-gx 0.5.0 (1/1) (0/1) (1/1) (0/1) True True
necat 667.0 95.0 necat Error correction and de-novo assembly for ONT Nanopore reads necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. De-novo assembly Sequence assembly Up-to-date https://github.com/xiaochuanle/NECAT Assembly necat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat 0.0.1_update20200803 necat 0.0.1_update20200803 (0/1) (0/1) (1/1) (0/1) True False
newick_utils 25505.0 448.0 newick_display Perform operations on Newick trees newick_utilities newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science To update http://cegg.unige.ch/newick_utils Visualization, Metagenomics newick_utils iuc https://github.com/tjunier/newick_utils https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils 1.6+galaxy1 newick_utils 1.6 (1/1) (1/1) (1/1) (1/1) True True
nextclade 3527.0 169.0 nextalign, nextclade Identify differences between your sequences and a reference sequence used by Nextstrain nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics To update https://github.com/nextstrain/nextclade Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade 2.7.0 nextalign 2.14.0 (1/2) (1/2) (2/2) (2/2) True True
@@ -505,12 +505,12 @@ novoplasty 6384.0 162.0 novoplasty NOVOPlasty is a de novo assembler and heterop
nugen_nudup nugen_nudup Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. Duplication detection Sequencing Up-to-date https://github.com/tecangenomics/nudup SAM, Metagenomics, Sequence Analysis, Transcriptomics nugen_nudup iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/nugen_nudup https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup 2.3.3 nudup 2.3.3 (0/1) (0/1) (0/1) (0/1) True True
obitools obi_illumina_pairend, obi_ngsfilter, obi_annotate, obi_clean, obi_convert, obi_grep, obi_sort, obi_stat, obi_tab, obi_uniq OBITools is a set of programs developed to simplify the manipulation of sequence files obitools obitools OBITools Set of python programs developed to simplify the manipulation of sequence files. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of DNA Metabarcoding. Sequence analysis, Sequence analysis Sequence analysis, DNA, Sequencing Up-to-date http://metabarcoding.org/obitools Sequence Analysis obitools iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools 1.2.13 obitools 1.2.13 (0/10) (10/10) (10/10) (10/10) True True
odgi odgi_build, odgi_viz Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. To update https://github.com/vgteam/odgi Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi 0.3 odgi 0.8.6 (0/2) (0/2) (2/2) (2/2) True False
-omark omark Proteome quality assessment software omark omark OMArk Proteome quality assessment software Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability To update https://github.com/DessimozLab/OMArk Sequence Analysis omark iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark 0.3.0 (0/1) (0/1) (1/1) (1/1) False
+omark omark Proteome quality assessment software omark omark OMArk Proteome quality assessment software Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability To update https://github.com/DessimozLab/OMArk Sequence Analysis omark iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark 0.3.0 (0/1) (0/1) (1/1) (1/1) True True
ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. To update https://github.com/nanoporetech/ont_fast5_api/ Nanopore ont_fast5_api iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ont_fast5_api https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api 3.1.3 ont-fast5-api 4.1.3 (0/4) (0/4) (4/4) (0/4) True False
optitype 321.0 24.0 optitype Precision HLA typing from NGS data Up-to-date https://github.com/FRED-2/OptiType Sequence Analysis optitype iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/optitype1 https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype 1.3.5 optitype 1.3.5 (0/1) (0/1) (1/1) (0/1) True False
orfipy 774.0 53.0 orfipy Galaxy wrapper for ORFIPY orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Up-to-date https://github.com/urmi-21/orfipy Sequence Analysis orfipy iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy 0.0.4 orfipy 0.0.4 (1/1) (0/1) (1/1) (0/1) True True
orthofinder orthofinder_onlygroups Accurate inference of orthologous gene groups made easy OrthoFinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Up-to-date https://github.com/davidemms/OrthoFinder Phylogenetics, Sequence Analysis orthofinder iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/orthofinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder 2.5.5 orthofinder 2.5.5 (0/1) (1/1) (1/1) (1/1) True True
-pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing Up-to-date https://pairtools.readthedocs.io Sequence Analysis pairtools iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 1.1.0 pairtools 1.1.0 (5/5) (0/5) (5/5) (0/5) False
+pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats Flexible tools for Hi-C data processing Up-to-date https://pairtools.readthedocs.io Sequence Analysis pairtools iuc https://github.com/open2c/pairtools https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools 1.1.0 pairtools 1.1.0 (5/5) (0/5) (5/5) (0/5) True False
pangolin 7276.0 259.0 pangolin Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. pangolin_cov-lineages pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages Tree-based sequence alignment, Variant classification Virology Up-to-date https://github.com/cov-lineages/pangolin Sequence Analysis pangolin iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin 4.3 pangolin 4.3 (1/1) (1/1) (1/1) (1/1) True False
parse_mito_blast 90.0 31.0 parse_mito_blast Filtering blast out from querying assembly against mitochondrial database. Up-to-date https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py Sequence Analysis parse_mito_blast iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/parse_mito_blast https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast 1.0.2 parse_mito_blast 1.0.2 (1/1) (1/1) (1/1) (0/1) True False
pathview 5260.0 565.0 pathview Pathview is a tool set for pathway based data integration and visualization. pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation To update https://bioconductor.org/packages/release/bioc/html/pathview.html Statistics, RNA, Micro-array Analysis pathview iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pathview https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview 1.34.0 bioconductor-pathview 1.42.0 (1/1) (1/1) (1/1) (1/1) True False
@@ -523,11 +523,11 @@ picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trai
picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing To update https://github.com/picrust/picrust2/wiki Metagenomics picrust2 iuc https://github.com/picrust/picrust2 https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 2.5.1 picrust2 2.5.2 (0/7) (7/7) (7/7) (0/7) True True
plasflow 22589.0 278.0 PlasFlow PlasFlow - Prediction of plasmid sequences in metagenomic contigs. plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. Sequence analysis Metagenomics Up-to-date https://github.com/smaegol/PlasFlow Sequence Analysis plasflow iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/plasflow https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow 1.1.0 plasflow 1.1.0 (1/1) (1/1) (1/1) (0/1) True True
plasmidfinder 22.0 8.0 plasmidfinder """PlasmidFinder provides the detection of replicons in the WGSand assigns the plasmids under study to lineages that trace backthe information to the existing knowledge on Inc groups and suggestspossible reference plasmids for each lineage""" PlasmidFinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Up-to-date https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ Sequence Analysis plasmidfinder iuc https://github.com/galaxyproject/tools-iuc/blob/master/tools/plasmidfinder https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder 2.1.6 plasmidfinder 2.1.6 (0/1) (0/1) (1/1) (1/1) True True
-polypolish 239.0 24.0 polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish 0.5.0 polypolish 0.6.0 (0/1) (0/1) (1/1) (1/1) True False
+polypolish 239.0 24.0 polypolish """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" Polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping To update https://github.com/rrwick/Polypolish Sequence Analysis polypolish iuc https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish 0.5.0 polypolish 0.6.0 (0/1) (0/1) (1/1) (1/1) True True
presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 pRESTO toolkit for immune repertoire analysis. presto presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. Nucleic acid sequence analysis Sequencing, DNA, Immunology To update https://presto.readthedocs.io/ Sequence Analysis presto iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto 0.6.2 presto 0.7.2 (11/11) (0/11) (0/11) (0/11) True False
pretext pretext_graph, pretext_map, pretext_snapshot Process genome contacts maps processing images. Up-to-date https://github.com/wtsi-hpag/PretextSnapshot Sequence Analysis suite_pretext iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext 0.0.6 pretextgraph 0.0.6 (3/3) (2/3) (3/3) (0/3) True False
prinseq 7881.0 70.0 prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics To update http://prinseq.sourceforge.net/manual.html Fastq Manipulation, Metagenomics prinseq iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prinseq/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq @TOOL_VERSION+galaxy2 prinseq 0.20.4 (1/1) (0/1) (1/1) (1/1) True False
-prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 (0/1) (0/1) (1/1) (1/1) False
+prodigal prodigal A protein-coding gene prediction software tool for bacterial and archaeal genomes prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. Genome annotation Genomics, Sequence analysis Up-to-date https://github.com/hyattpd/Prodigal Genome annotation prodigal iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal 2.6.3 prodigal 2.6.3 (0/1) (0/1) (1/1) (1/1) True True
progressivemauve 1734.0 286.0 progressivemauve, xmfa2gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner To update Sequence Analysis progressivemauve iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve progressivemauve snapshot_2015_02_13 (2/2) (0/2) (2/2) (0/2) True False
prokka 371445.0 3233.0 prokka Rapid annotation of prokaryotic genomes prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. Gene prediction, Coding region prediction, Genome annotation Genomics, Model organisms, Virology Up-to-date http://github.com/tseemann/prokka Sequence Analysis prokka crs4 https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka 1.14.6 prokka 1.14.6 (1/1) (1/1) (1/1) (1/1) True True
prot-scriber prot_scriber Protein annotation of short human readable descriptions To update https://github.com/usadellab/prot-scriber Proteomics prot_scriber iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber 0.1.4 prot-scriber 0.1.5 (0/1) (0/1) (1/1) (0/1) True False
@@ -553,7 +553,7 @@ recentrifuge 331.0 48.0 recentrifuge """With Recentrifuge, researchers can analy
red 578.0 88.0 red Red (REpeat Detector) red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation Up-to-date https://github.com/BioinformaticsToolsmith/Red Sequence Analysis red iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/red https://github.com/galaxyproject/tools-iuc/tree/main/tools/red 2018.09.10 red 2018.09.10 (1/1) (1/1) (1/1) (1/1) True False
repeatmasker repeatmasker_wrapper RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Genome annotation Sequence analysis, Sequence composition, complexity and repeats Up-to-date http://www.repeatmasker.org/ Sequence Analysis repeat_masker bgruening https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmasker https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker 4.1.5 repeatmasker 4.1.5 (1/1) (1/1) (1/1) (1/1) True False
repeatmodeler 1177.0 217.0 repeatmodeler RepeatModeler - Model repetitive DNA repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats To update https://www.repeatmasker.org/RepeatModeler/ Genome annotation repeatmodeler csbl https://github.com/galaxyproject/tools-iuc/tree/master/tools/repeatmodeler https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler 2.0.5 (1/1) (1/1) (1/1) (1/1) True False
-revoluzer revoluzer_crex, revoluzer_distmat revoluzer wrappers revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc Structural variation detection Molecular evolution, Phylogeny Up-to-date https://gitlab.com/Bernt/revoluzer/ Phylogenetics revoluzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer 0.1.6 revoluzer 0.1.6 (0/2) (0/2) (2/2) (0/2) False
+revoluzer revoluzer_crex, revoluzer_distmat revoluzer wrappers revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc Structural variation detection Molecular evolution, Phylogeny Up-to-date https://gitlab.com/Bernt/revoluzer/ Phylogenetics revoluzer iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer 0.1.6 revoluzer 0.1.6 (0/2) (0/2) (2/2) (0/2) True False
ribowaltz ribowaltz_process, ribowaltz_plot Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data riboWaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Computational biology To update https://github.com/LabTranslationalArchitectomics/riboWaltz Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/ribowaltz https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz 1.2.0 ribowaltz 2.0 (0/2) (0/2) (2/2) (0/2) True False
rnaquast 1110.0 109.0 rna_quast rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. rnaQUAST rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-seq Up-to-date https://github.com/ablab/rnaquast Assembly, RNA rnaquast iuc https://git.ufz.de/lehmanju/rnaquast https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast 2.2.3 rnaquast 2.2.3 (1/1) (0/1) (1/1) (1/1) True False
roary 12225.0 656.0 roary Roary the pangenome pipeline roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. Genome assembly DNA, Genomics, Mapping Up-to-date https://sanger-pathogens.github.io/Roary/ Sequence Analysis roary iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/roary https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary 3.13.0 roary 3.13.0 (1/1) (1/1) (1/1) (1/1) True True
@@ -578,7 +578,7 @@ seqtk 59668.0 753.0 seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_het
seqwish 271.0 seqwish Alignment to variation graph inducer To update https://github.com/ekg/seqwish Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqwish/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish 0.7.5 seqwish 0.7.10 (0/1) (0/1) (1/1) (0/1) True False
seurat 1543.0 66.0 seurat A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data To update https://github.com/satijalab/seurat Transcriptomics, RNA, Statistics seurat iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/seurat https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat 4.3.0.1 r-seurat 3.0.2 (1/1) (1/1) (1/1) (1/1) True False
shasta 763.0 154.0 shasta Fast de novo assembly of long read sequencing data To update https://github.com/chanzuckerberg/shasta Assembly, Nanopore shasta iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shasta https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta 0.6.0 shasta 0.11.1 (0/1) (1/1) (1/1) (0/1) True False
-shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah 1.1.3 shorah 1.99.2 (0/1) (0/1) (0/1) (0/1) True False
+shorah shorah_amplicon Reconstruct haplotypes using ShoRAH in amplicon mode shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics To update https://github.com/cbg-ethz/shorah/blob/master/README.md Sequence Analysis shorah_amplicon iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shorah https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah 1.1.3 shorah 1.99.2 (0/1) (0/1) (0/1) (0/1) True True
shovill 41600.0 1008.0 shovill Faster de novo assembly pipeline based around Spades shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. Genome assembly Genomics, Microbiology, Sequence assembly Up-to-date https://github.com/tseemann/shovill Assembly shovill iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill 1.1.0 shovill 1.1.0 (1/1) (1/1) (1/1) (1/1) True True
sickle 14982.0 269.0 sickle A windowed adaptive trimming tool for FASTQ files using quality sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. Sequence trimming Data quality management To update https://github.com/najoshi/sickle Fastq Manipulation, Sequence Analysis sickle iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle 1.33.2 sickle-trim 1.33 (1/1) (0/1) (1/1) (1/1) True False
sina 1128.0 42.0 sina SINA reference based multiple sequence alignment sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Up-to-date https://sina.readthedocs.io/en/latest/ Sequence Analysis sina iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/sina https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina 1.7.2 sina 1.7.2 (1/1) (0/1) (1/1) (0/1) True False
@@ -619,7 +619,7 @@ transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_
transtermhp 229.0 5.0 transtermhp Finds rho-independent transcription terminators in bacterial genomes transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator Transcriptional regulatory element prediction Transcription factors and regulatory sites To update https://transterm.cbcb.umd.edu Sequence Analysis transtermhp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp transtermhp 2.09 (1/1) (0/1) (1/1) (0/1) True True
trinity 12733.0 678.0 trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Up-to-date https://github.com/trinityrnaseq/trinityrnaseq Transcriptomics, RNA iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity 2.15.1 trinity 2.15.1 (9/13) (13/13) (13/13) (13/13) True False
trinotate 1796.0 151.0 trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Gene functional annotation Gene expression, Transcriptomics To update https://trinotate.github.io/ Transcriptomics, RNA trinotate iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinotate https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate 3.2.2 trinotate 4.0.2 (1/1) (1/1) (1/1) (0/1) True False
-trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 (0/5) (5/5) (5/5) (5/5) True False
+trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample Trycycler toolkit wrappers Up-to-date https://github.com/rrwick/Trycycler Assembly trycycler iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler 0.5.5 trycycler 0.5.5 (0/5) (5/5) (5/5) (5/5) True True
tsebra 5.0 tsebra This tool has been developed to combine BRAKER predictions. tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Up-to-date https://github.com/Gaius-Augustus/TSEBRA Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra 1.1.2.4 tsebra 1.1.2.4 (0/1) (0/1) (1/1) (1/1) True False
ucsc_blat ucsc_blat Standalone blat sequence search command line tool blat blat BLAT Fast, accurate spliced alignment of DNA sequences. Sequence alignment Sequence analysis To update http://genome.ucsc.edu/goldenPath/help/blatSpec.html Sequence Analysis ucsc_blat yating-l https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat 377 ucsc-blat 445 (0/1) (0/1) (0/1) (0/1) True False
umi_tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist UMI-tools extract - Extract UMIs from fastq umi-tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs To update https://github.com/CGATOxford/UMI-tools Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools 1.1.2 umi_tools 1.1.5 (5/5) (5/5) (5/5) (5/5) True False
@@ -633,12 +633,12 @@ velvet 12218.0 1280.0 velvetg, velveth de novo genomic assembler specially desig
velvet_optimiser velvetoptimiser Automatically optimize Velvet assemblies velvetoptimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. Optimisation and refinement, Sequence assembly Genomics, Sequence assembly To update Assembly velvetoptimiser simon-gladman https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvetoptimiser https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser 2.2.6+galaxy2 velvet 1.2.10 (1/1) (1/1) (1/1) (0/1) True True
verkko 22.0 9.0 verkko Telomere-to-telomere assembly pipeline To update https://github.com/marbl/verkko Assembly verkko iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/verkko https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko 1.3.1 verkko 2.0 (0/1) (0/1) (1/1) (0/1) True False
vg vg_convert, vg_deconstruct, vg_view Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods To update https://github.com/vgteam/vg Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg 1.23.0 vg 1.56.0 (0/3) (0/3) (3/3) (3/3) True False
-virAnnot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers To update https://github.com/marieBvr/virAnnot Metagenomics virannot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot 1.0.0+galaxy0 biopython 1.70 (0/3) (0/3) (3/3) (3/3) False
+virAnnot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv virAnnot wrappers To update https://github.com/marieBvr/virAnnot Metagenomics virannot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot https://github.com/galaxyproject/tools-iuc/tree/main/tools/virAnnot 1.0.0+galaxy0 biopython 1.70 (0/3) (0/3) (3/3) (3/3) True True
volcanoplot 30946.0 1749.0 volcanoplot Tool to create a Volcano Plot To update Visualization, Transcriptomics, Statistics volcanoplot iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot 0.0.5 r-ggplot2 2.2.1 (1/1) (1/1) (1/1) (1/1) True False
vsearch 8507.0 182.0 vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. DNA mapping, Chimera detection Metagenomics, Sequence analysis To update https://github.com/torognes/vsearch Sequence Analysis vsearch iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsearch https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch 2.8.3 vsearch 2.28.1 (8/8) (8/8) (8/8) (8/8) True True
vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. To update https://github.com/USDA-VS/vSNP Sequence Analysis vsnp iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp 3.0.6 pysam 0.22.1 (0/5) (0/5) (0/5) (0/5) True False
weather_app simple_weather provides simple weather in text format To update http://wttr.in/ Visualization, Web Services simpleweather iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/weather_app https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app 0.1.2 curl (0/1) (0/1) (0/1) (0/1) True False
-windowmasker 85.0 windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker 1.0 blast 2.15.0 (0/2) (2/2) (2/2) (0/2) False
+windowmasker 85.0 windowmasker_mkcounts, windowmasker_ustat Identify repetitive regions using WindowMasker To update https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ Sequence Analysis windowmasker iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/ https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker 1.0 blast 2.15.0 (0/2) (2/2) (2/2) (0/2) True False
yahs 344.0 64.0 yahs Yet Another Hi-C scaffolding tool Up-to-date https://github.com/c-zhou/yahs Assembly yahs iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/yahs https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs 1.2a.2 yahs 1.2a.2 (1/1) (1/1) (1/1) (0/1) True False
bamtools 14039.0 208.0 bamtools Operate on and transform BAM datasets in various ways using bamtools bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools 2.5.2 bamtools 2.5.2 (1/1) (0/1) (1/1) (1/1) True True
bamtools_filter 114845.0 1195.0 bamFilter Filter BAM datasets on various attributes using bamtools filter bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Up-to-date https://github.com/pezmaster31/bamtools Sequence Analysis, SAM bamtools_filter devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter 2.5.2 bamtools 2.5.2 (1/1) (1/1) (1/1) (1/1) True False
@@ -646,30 +646,30 @@ bamtools_split 1434.0 47.0 bamtools_split_mapped, bamtools_split_paired, bamtool
biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. Sequence analysis Mobile genetic elements, Workflows Up-to-date https://www.sanger.ac.uk/science/tools/bio-tradis Genome annotation biotradis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis 1.4.5 biotradis 1.4.5 (3/3) (0/3) (0/3) (0/3) True True
kraken 13938.0 404.0 kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken devteam https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken kraken 1.1.1 (5/5) (5/5) (5/5) (5/5) True True
kraken2 185308.0 2367.0 kraken2 Kraken2 for taxonomic designation. kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Taxonomic classification Taxonomy, Metagenomics To update http://ccb.jhu.edu/software/kraken/ Metagenomics kraken2 iuc https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 2.1.1 kraken2 2.1.3 (1/1) (1/1) (1/1) (1/1) True True
-suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) False
-suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) False
-suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) False
-suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) False
-suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.2.0+q2galaxy.2024.2.1 (21/22) (21/22) (21/22) (21/22) False
-suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) False
-suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.2.0+q2galaxy.2024.2.1 (10/11) (10/11) (10/11) (10/11) False
-suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.2.2+q2galaxy.2024.2.1 (17/22) (17/22) (17/22) (17/22) False
-suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) False
-suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) False
-suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) False
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-suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) False
+suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True True
+suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) True True
+suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True True
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+suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True True
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+suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True True
+suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.2.0+q2galaxy.2024.2.1 (10/11) (10/11) (10/11) (10/11) True True
+suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.2.2+q2galaxy.2024.2.1 (17/22) (17/22) (17/22) (17/22) True True
+suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True True
+suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) True True
+suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) True True
+suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) True True
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+suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) True True
suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) False
-suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) False
-suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) False
-suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) False
-suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) False
-suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) False
-frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) False
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+suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True True
+suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) True True
+suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) True True
+suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) True True
+frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) True True
ThermoRawFileParser thermo_raw_file_converter Thermo RAW file converter To update https://github.com/compomics/ThermoRawFileParser Proteomics thermo_raw_file_converter galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawFileParser 1.3.4 thermorawfileparser 1.4.4 (0/1) (1/1) (1/1) (0/1) True False
bed_to_protein_map 385.0 49.0 bed_to_protein_map Converts a BED file to a tabular list of exon locations To update Proteomics bed_to_protein_map galaxyp https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bed_to_protein_map 0.2.0 python (1/1) (1/1) (1/1) (0/1) True False
blast_plus_remote_blastp blast_plus_remote_blastp NCBI BLAST+ with -remote option To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis blast_plus_remote_blastp galaxyp https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/blast_plus_remote_blastp 2.6.0 blast 2.15.0 (0/1) (0/1) (0/1) (0/1) True False
@@ -776,21 +776,21 @@ xpore xpore_dataprep, xpore_diffmod Identification and quantification of diffe
yac_clipper yac Clips 3' adapters for small RNA sequencing reads. To update http://artbio.fr RNA, Fastq Manipulation yac_clipper artbio https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper https://github.com/ARTbio/tools-artbio/tree/main/tools/yac_clipper 2.5.1 python (0/1) (0/1) (0/1) (0/1) True False
EMLassemblyline eal_table_template, eal_templates, eml2eal, entities_template, geo_cov_template, makeeml, raster_template, taxo_cov_template, vector_template Tools using EML Assembly Line R package to generate EML metadata from template metadata files and vice versa To update https://github.com/EDIorg/EMLassemblyline Ecology emlassemblyline ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline https://github.com/galaxyecology/tools-ecology/tree/master/tools/EMLassemblyline 0.1.1+galaxy0 r-emlassemblyline (0/9) (0/9) (9/9) (9/9) True False
Ecoregionalization_workflow ecoregion_brt_analysis, ecoregion_GeoNearestNeighbor, ecoregion_cluster_estimate, ecoregion_clara_cluster, ecoregion_eco_map, ecoregion_taxa_seeker Tools to compute ecoregionalization with BRT model predictions and clustering. To update https://github.com/PaulineSGN/Workflow_Galaxy Ecology ecoregionalization ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow 0.1.0+galaxy0 r-base (0/6) (0/6) (6/6) (5/6) True False
-Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base (0/3) (0/3) (3/3) (3/3) False
+Geom_mean_workflow Map_shp, Mean_geom, bar_plot Tools to compute The evolution of the total volume of very large trees, standing dead wood and dead wood on the ground on an area and the rate of devolution of the volume of wood favorable to biodiversity by large ecological regions (France). To update https://github.com/PaulineSGN/Galaxy_tool_moyenne_geom Ecology Geometric means (Dead wood) ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow https://github.com/galaxyecology/tools-ecology/tree/master/tools/Geom_mean_workflow 0.1.0+galaxy0 r-base (0/3) (0/3) (3/3) (3/3) True False
PAMPA pampa_communitymetrics, pampa_presabs, pampa_glmcomm, pampa_glmsp, pampa_plotglm Tools to compute and analyse biodiversity metrics To update Ecology pampa ecology https://github.com/ColineRoyaux/PAMPA-Galaxy https://github.com/galaxyecology/tools-ecology/tree/master/tools/PAMPA 0.0.2 (0/5) (5/5) (5/5) (5/5) True True
champ_blocs cb_dissim, cb_ivr, cb_div Compute indicators for turnover boulders fields To update Ecology ecology https://github.com/Marie59/champ_blocs https://github.com/galaxyecology/tools-ecology/tree/master/tools/champ_blocs 0.0.0 r-base (0/3) (0/3) (3/3) (3/3) True False
consensus_from_alignments aligned_to_consensus Tool to compute a consensus sequence from several aligned fasta sequences To update Sequence Analysis consalign ecology https://github.com/ColineRoyaux/Galaxy_tool_projects/tree/main/consensus_from_alignments https://github.com/galaxyecology/tools-ecology/tree/master/tools/consensus_from_alignments 1.0.0 r-bioseq (0/1) (0/1) (1/1) (1/1) True False
data_exploration tool_anonymization, ecology_homogeneity_normality, ecology_beta_diversity, ecology_link_between_var, ecology_presence_abs_abund, ecology_stat_presence_abs Explore data through multiple statistical tools To update Ecology ecology https://github.com/Marie59/Data_explo_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_exploration 0.0.0 r-tangles (0/6) (0/6) (6/6) (6/6) True False
xarray timeseries_extraction, xarray_coords_info, xarray_mapplot, xarray_metadata_info, xarray_netcdf2netcdf, xarray_select xarray (formerly xray) is an open source project and Python package that makes working withlabelled multi-dimensional arrays simple, efficient, and fun!xarray integrates with Dask to support parallel computations and streaming computation on datasetsthat don’t fit into memory. To update http://xarray.pydata.org Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray 2022.3.0 xarray (5/6) (2/6) (6/6) (5/6) True False
gdal gdal_gdal_merge, gdal_gdal_translate, gdal_gdaladdo, gdal_gdalbuildvrt, gdal_gdalinfo, gdal_gdalwarp, gdal_ogr2ogr, gdal_ogrinfo Geospatial Data Abstraction Library tools are all dedicated to manipulate raster and vector geospatial data formats. To update https://www.gdal.org Ecology gdal ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal https://github.com/galaxyecology/tools-ecology/tree/master/tools/gdal 3.0.0 (0/8) (0/8) (8/8) (8/8) True False
-interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt (0/1) (0/1) (1/1) (0/1) False
-medenv iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa To update https://github.com/jeremyfix/medenv Ecology, Data Source ecology https://github.com/jeremyfix/medenv https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv 0.1.0 pandas (0/1) (0/1) (1/1) (0/1) False
+interpolation interpolation_run_idw_interpolation Run IDW interpolation based on a .csv and .geojson file To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation 1.0 r-getopt (0/1) (0/1) (1/1) (0/1) True False
+medenv iabiodiv_smartbiodiv_med_environ Retrieve environmental data from etopo, cmems and woa To update https://github.com/jeremyfix/medenv Ecology, Data Source ecology https://github.com/jeremyfix/medenv https://github.com/galaxyecology/tools-ecology/tree/master/tools/medenv 0.1.0 pandas (0/1) (0/1) (1/1) (0/1) True False
obisindicators 45.0 4.0 obisindicators, obis_data Compute biodiveristy indicators for marine data from obis To update https://github.com/Marie59/obisindicators Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators https://github.com/galaxyecology/tools-ecology/tree/master/tools/obisindicators 0.0.2 r-base (1/2) (0/2) (2/2) (1/2) True True
-ocean argo_getdata Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 (0/1) (0/1) (1/1) (0/1) False
-ogcProcess_otb_bandmath otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath 1.0 r-base (0/1) (0/1) (1/1) (0/1) False
-ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing 1.0 r-base (0/1) (0/1) (1/1) (0/1) False
+ocean argo_getdata Access, process, visualise oceanographic data for the Earth System To update https://github.com/Marie59/FE-ft-ESG/tree/main/argo Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean https://github.com/galaxyecology/tools-ecology/tree/master/tools/ocean 0.1.15 (0/1) (0/1) (1/1) (0/1) True False
+ogcProcess_otb_bandmath otb_band_math Outputs a monoband image which is the result of a mathematical operation on several multi-band images. To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/OtbBandMath https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_bandmath 1.0 r-base (0/1) (0/1) (1/1) (0/1) True False
+ogcProcess_otb_meanShiftSmoothing otb_mean_shift_smoothing This application smooths an image using the MeanShift algorithm. To update https://github.com/AquaINFRA/galaxy Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/interpolation https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogcProcess_otb_meanShiftSmoothing 1.0 r-base (0/1) (0/1) (1/1) (0/1) True False
regionalgam regionalgam_ab_index, regionalgam_autocor_acf, regionalgam_flight_curve, regionalgam_glmmpql, regionalgam_gls_adjusted, regionalgam_gls, regionalgam_plot_trend To update https://github.com/RetoSchmucki/regionalGAM Ecology ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam https://github.com/galaxyecology/tools-ecology/tree/master/tools/regionalgam 1.5 r-mgcv (0/7) (0/7) (7/7) (7/7) True False
-sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. To update https://cran.r-project.org/web/packages/sdmpredictors/index.html Ecology sdmpredictors ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0.2.15 r-base (0/1) (0/1) (0/1) (0/1) False
+sdmpredictors sdmpredictors_list_layers Terrestrial and marine predictors for species distribution modelling. To update https://cran.r-project.org/web/packages/sdmpredictors/index.html Ecology sdmpredictors ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors https://github.com/galaxyecology/tools-ecology/tree/master/tools/sdmpredictors 0.2.15 r-base (0/1) (0/1) (0/1) (0/1) True False
spocc spocc_occ Get species occurences data To update https://cran.r-project.org/web/packages/spocc/index.html Ecology spocc_occ ecology https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc https://github.com/galaxyecology/tools-ecology/tree/master/tools/spocc 1.2.2 (0/1) (0/1) (1/1) (1/1) True False
srs_tools srs_diversity_maps, srs_global_indices, srs_process_data, srs_spectral_indices, srs_pca, srs_preprocess_s2, srs_metadata Compute biodiversity indicators for remote sensing data from Sentinel 2 To update Ecology ecology https://github.com/Marie59/Sentinel_2A/srs_tools https://github.com/galaxyecology/tools-ecology/tree/master/tools/srs_tools 0.0.1 r-base (4/7) (0/7) (7/7) (7/7) True False
stoc stoceps_filteringsp, stoceps_glm, stoceps_glm_group, stoceps_maketablecarrer, stoceps_trend_indic Tools to analyse STOC data. To update Ecology stoceps ecology https://github.com/Alanamosse/Galaxy-E/tree/stoctool/tools/stoc https://github.com/galaxyecology/tools-ecology/tree/master/tools/stoc 0.0.2 (0/5) (0/5) (5/5) (5/5) True False
@@ -831,27 +831,27 @@ blast_rbh 22499.0 121.0 blast_reciprocal_best_hits BLAST Reciprocal Best Hits (R
blastxml_to_top_descr 264558.0 159.0 blastxml_to_top_descr Make table of top BLAST match descriptions To update https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr Convert Formats, Sequence Analysis, Text Manipulation blastxml_to_top_descr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr https://github.com/peterjc/galaxy_blast/tree/master/tools/blastxml_to_top_descr 0.1.2 python (0/1) (0/1) (1/1) (0/1) True True
make_nr make_nr Make a FASTA file non-redundant To update https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr Fasta Manipulation, Sequence Analysis make_nr peterjc https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr https://github.com/peterjc/galaxy_blast/tree/master/tools/make_nr 0.0.2 biopython 1.70 (0/1) (0/1) (0/1) (0/1) True True
ncbi_blast_plus 365597.0 4066.0 blastxml_to_tabular, get_species_taxids, ncbi_blastdbcmd_info, ncbi_blastdbcmd_wrapper, ncbi_blastn_wrapper, ncbi_blastp_wrapper, ncbi_blastx_wrapper, ncbi_convert2blastmask_wrapper, ncbi_deltablast_wrapper, ncbi_dustmasker_wrapper, ncbi_makeblastdb, ncbi_makeprofiledb, ncbi_psiblast_wrapper, ncbi_rpsblast_wrapper, ncbi_rpstblastn_wrapper, ncbi_segmasker_wrapper, ncbi_tblastn_wrapper, ncbi_tblastx_wrapper NCBI BLAST+ To update https://blast.ncbi.nlm.nih.gov/ Sequence Analysis ncbi_blast_plus devteam https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus 2.14.1 python (16/18) (16/18) (16/18) (16/18) True True
-suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) False
-suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) False
-suite_qiime2__dada2 qiime2__dada2__denoise_ccs, qiime2__dada2__denoise_paired, qiime2__dada2__denoise_pyro, qiime2__dada2__denoise_single To update http://benjjneb.github.io/dada2/ Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) False
-suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__demux qiime2__demux__emp_paired, qiime2__demux__emp_single, qiime2__demux__filter_samples, qiime2__demux__partition_samples_paired, qiime2__demux__partition_samples_single, qiime2__demux__subsample_paired, qiime2__demux__subsample_single, qiime2__demux__summarize, qiime2__demux__tabulate_read_counts To update https://github.com/qiime2/q2-demux Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux 2024.2.0+q2galaxy.2024.2.1 (6/9) (6/9) (6/9) (6/9) False
-suite_qiime2__diversity qiime2__diversity__adonis, qiime2__diversity__alpha, qiime2__diversity__alpha_correlation, qiime2__diversity__alpha_group_significance, qiime2__diversity__alpha_phylogenetic, qiime2__diversity__alpha_rarefaction, qiime2__diversity__beta, qiime2__diversity__beta_correlation, qiime2__diversity__beta_group_significance, qiime2__diversity__beta_phylogenetic, qiime2__diversity__beta_rarefaction, qiime2__diversity__bioenv, qiime2__diversity__core_metrics, qiime2__diversity__core_metrics_phylogenetic, qiime2__diversity__filter_distance_matrix, qiime2__diversity__mantel, qiime2__diversity__partial_procrustes, qiime2__diversity__pcoa, qiime2__diversity__pcoa_biplot, qiime2__diversity__procrustes_analysis, qiime2__diversity__tsne, qiime2__diversity__umap To update https://github.com/qiime2/q2-diversity Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity 2024.2.0+q2galaxy.2024.2.1 (21/22) (21/22) (21/22) (21/22) False
-suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) False
-suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__feature_classifier qiime2__feature_classifier__blast, qiime2__feature_classifier__classify_consensus_blast, qiime2__feature_classifier__classify_consensus_vsearch, qiime2__feature_classifier__classify_hybrid_vsearch_sklearn, qiime2__feature_classifier__classify_sklearn, qiime2__feature_classifier__extract_reads, qiime2__feature_classifier__find_consensus_annotation, qiime2__feature_classifier__fit_classifier_naive_bayes, qiime2__feature_classifier__fit_classifier_sklearn, qiime2__feature_classifier__makeblastdb, qiime2__feature_classifier__vsearch_global To update https://github.com/qiime2/q2-feature-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier 2024.2.0+q2galaxy.2024.2.1 (10/11) (10/11) (10/11) (10/11) False
-suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.2.2+q2galaxy.2024.2.1 (17/22) (17/22) (17/22) (17/22) False
-suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) False
-suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) False
-suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) False
-suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) False
-suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) False
-suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) False
+suite_qiime2__alignment qiime2__alignment__mafft, qiime2__alignment__mafft_add, qiime2__alignment__mask To update https://github.com/qiime2/q2-alignment Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__alignment 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True True
+suite_qiime2__composition qiime2__composition__add_pseudocount, qiime2__composition__ancom, qiime2__composition__ancombc, qiime2__composition__da_barplot, qiime2__composition__tabulate To update https://github.com/qiime2/q2-composition Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition 2024.2.0+q2galaxy.2024.2.1 (4/5) (4/5) (4/5) (2/5) True True
+suite_qiime2__cutadapt qiime2__cutadapt__demux_paired, qiime2__cutadapt__demux_single, qiime2__cutadapt__trim_paired, qiime2__cutadapt__trim_single To update https://github.com/qiime2/q2-cutadapt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True True
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+suite_qiime2__deblur qiime2__deblur__denoise_16S, qiime2__deblur__denoise_other, qiime2__deblur__visualize_stats To update https://github.com/biocore/deblur Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True True
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+suite_qiime2__diversity_lib qiime2__diversity_lib__alpha_passthrough, qiime2__diversity_lib__beta_passthrough, qiime2__diversity_lib__beta_phylogenetic_meta_passthrough, qiime2__diversity_lib__beta_phylogenetic_passthrough, qiime2__diversity_lib__bray_curtis, qiime2__diversity_lib__faith_pd, qiime2__diversity_lib__jaccard, qiime2__diversity_lib__observed_features, qiime2__diversity_lib__pielou_evenness, qiime2__diversity_lib__shannon_entropy, qiime2__diversity_lib__unweighted_unifrac, qiime2__diversity_lib__weighted_unifrac To update https://github.com/qiime2/q2-diversity-lib Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) True True
+suite_qiime2__emperor qiime2__emperor__biplot, qiime2__emperor__plot, qiime2__emperor__procrustes_plot To update http://emperor.microbio.me Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True True
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+suite_qiime2__feature_table qiime2__feature_table__core_features, qiime2__feature_table__filter_features, qiime2__feature_table__filter_features_conditionally, qiime2__feature_table__filter_samples, qiime2__feature_table__filter_seqs, qiime2__feature_table__group, qiime2__feature_table__heatmap, qiime2__feature_table__merge, qiime2__feature_table__merge_seqs, qiime2__feature_table__merge_taxa, qiime2__feature_table__presence_absence, qiime2__feature_table__rarefy, qiime2__feature_table__relative_frequency, qiime2__feature_table__rename_ids, qiime2__feature_table__split, qiime2__feature_table__subsample_ids, qiime2__feature_table__summarize, qiime2__feature_table__summarize_plus, qiime2__feature_table__tabulate_feature_frequencies, qiime2__feature_table__tabulate_sample_frequencies, qiime2__feature_table__tabulate_seqs, qiime2__feature_table__transpose To update https://github.com/qiime2/q2-feature-table Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table 2024.2.2+q2galaxy.2024.2.1 (17/22) (17/22) (17/22) (17/22) True True
+suite_qiime2__fragment_insertion qiime2__fragment_insertion__classify_otus_experimental, qiime2__fragment_insertion__filter_features, qiime2__fragment_insertion__sepp To update https://github.com/qiime2/q2-fragment-insertion Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion 2024.2.0+q2galaxy.2024.2.1 (3/3) (3/3) (3/3) (3/3) True True
+suite_qiime2__longitudinal qiime2__longitudinal__anova, qiime2__longitudinal__feature_volatility, qiime2__longitudinal__first_differences, qiime2__longitudinal__first_distances, qiime2__longitudinal__linear_mixed_effects, qiime2__longitudinal__maturity_index, qiime2__longitudinal__nmit, qiime2__longitudinal__pairwise_differences, qiime2__longitudinal__pairwise_distances, qiime2__longitudinal__plot_feature_volatility, qiime2__longitudinal__volatility To update https://github.com/qiime2/q2-longitudinal Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal 2024.2.0+q2galaxy.2024.2.1 (11/11) (11/11) (11/11) (11/11) True True
+suite_qiime2__metadata qiime2__metadata__distance_matrix, qiime2__metadata__merge, qiime2__metadata__shuffle_groups, qiime2__metadata__tabulate To update https://github.com/qiime2/q2-metadata Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__metadata 2024.2.0+q2galaxy.2024.2.1 (3/4) (3/4) (3/4) (3/4) True True
+suite_qiime2__phylogeny qiime2__phylogeny__align_to_tree_mafft_fasttree, qiime2__phylogeny__align_to_tree_mafft_iqtree, qiime2__phylogeny__align_to_tree_mafft_raxml, qiime2__phylogeny__fasttree, qiime2__phylogeny__filter_table, qiime2__phylogeny__filter_tree, qiime2__phylogeny__iqtree, qiime2__phylogeny__iqtree_ultrafast_bootstrap, qiime2__phylogeny__midpoint_root, qiime2__phylogeny__raxml, qiime2__phylogeny__raxml_rapid_bootstrap, qiime2__phylogeny__robinson_foulds To update https://github.com/qiime2/q2-phylogeny Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny 2024.2.0+q2galaxy.2024.2.1 (12/12) (12/12) (12/12) (12/12) True True
+suite_qiime2__quality_control qiime2__quality_control__bowtie2_build, qiime2__quality_control__decontam_identify, qiime2__quality_control__decontam_identify_batches, qiime2__quality_control__decontam_remove, qiime2__quality_control__decontam_score_viz, qiime2__quality_control__evaluate_composition, qiime2__quality_control__evaluate_seqs, qiime2__quality_control__evaluate_taxonomy, qiime2__quality_control__exclude_seqs, qiime2__quality_control__filter_reads To update https://github.com/qiime2/q2-quality-control Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control 2024.2.0+q2galaxy.2024.2.1 (6/10) (6/10) (6/10) (6/10) True True
+suite_qiime2__quality_filter qiime2__quality_filter__q_score To update https://github.com/qiime2/q2-quality-filter Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter 2024.2.0+q2galaxy.2024.2.1 (1/1) (1/1) (1/1) (1/1) True True
suite_qiime2__rescript qiime2__rescript__cull_seqs, qiime2__rescript__degap_seqs, qiime2__rescript__dereplicate, qiime2__rescript__edit_taxonomy, qiime2__rescript__evaluate_classifications, qiime2__rescript__evaluate_cross_validate, qiime2__rescript__evaluate_fit_classifier, qiime2__rescript__evaluate_seqs, qiime2__rescript__evaluate_taxonomy, qiime2__rescript__extract_seq_segments, qiime2__rescript__filter_seqs_length, qiime2__rescript__filter_seqs_length_by_taxon, qiime2__rescript__filter_taxa, qiime2__rescript__get_gtdb_data, qiime2__rescript__get_ncbi_data, qiime2__rescript__get_ncbi_data_protein, qiime2__rescript__get_ncbi_genomes, qiime2__rescript__get_silva_data, qiime2__rescript__get_unite_data, qiime2__rescript__merge_taxa, qiime2__rescript__orient_seqs, qiime2__rescript__parse_silva_taxonomy, qiime2__rescript__reverse_transcribe, qiime2__rescript__subsample_fasta, qiime2__rescript__trim_alignment To update https://github.com/nbokulich/RESCRIPt Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript 2024.2.2+q2galaxy.2024.2.1 (0/25) (0/25) (0/25) (0/25) False
-suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) False
-suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) False
-suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) False
-suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) False
-suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) False
-frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) False
+suite_qiime2__sample_classifier qiime2__sample_classifier__classify_samples, qiime2__sample_classifier__classify_samples_from_dist, qiime2__sample_classifier__classify_samples_ncv, qiime2__sample_classifier__confusion_matrix, qiime2__sample_classifier__fit_classifier, qiime2__sample_classifier__fit_regressor, qiime2__sample_classifier__heatmap, qiime2__sample_classifier__metatable, qiime2__sample_classifier__predict_classification, qiime2__sample_classifier__predict_regression, qiime2__sample_classifier__regress_samples, qiime2__sample_classifier__regress_samples_ncv, qiime2__sample_classifier__scatterplot, qiime2__sample_classifier__split_table, qiime2__sample_classifier__summarize To update https://github.com/qiime2/q2-sample-classifier Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__sample_classifier 2024.2.0+q2galaxy.2024.2.1 (15/15) (15/15) (15/15) (15/15) True True
+suite_qiime2__taxa qiime2__taxa__barplot, qiime2__taxa__collapse, qiime2__taxa__filter_seqs, qiime2__taxa__filter_table To update https://github.com/qiime2/q2-taxa Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa 2024.2.0+q2galaxy.2024.2.1 (4/4) (4/4) (4/4) (4/4) True True
+suite_qiime2__vsearch qiime2__vsearch__cluster_features_closed_reference, qiime2__vsearch__cluster_features_de_novo, qiime2__vsearch__cluster_features_open_reference, qiime2__vsearch__dereplicate_sequences, qiime2__vsearch__fastq_stats, qiime2__vsearch__merge_pairs, qiime2__vsearch__uchime_denovo, qiime2__vsearch__uchime_ref To update https://github.com/qiime2/q2-vsearch Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch 2024.2.0+q2galaxy.2024.2.1 (8/8) (8/8) (8/8) (7/8) True True
+suite_qiime2_core__tools qiime2_core__tools__export, qiime2_core__tools__import, qiime2_core__tools__import_fastq To update https://qiime2.org Metagenomics, Sequence Analysis, Statistics q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2_core__tools 2024.2.1+dist.he188c3c2 (2/3) (2/3) (2/3) (2/3) True True
+suite_qiime2_core To update Statistics, Metagenomics, Sequence Analysis q2d2 https://github.com/qiime2/galaxy-tools/tree/main/tool_collections/suite_qiime2_core (0/1) (0/1) (0/1) (0/1) True True
+frogs FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom Suite for metabarcoding analysis Up-to-date http://frogs.toulouse.inrae.fr/ Metagenomics frogs frogs https://github.com/geraldinepascal/FROGS-wrappers/ https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs 4.1.0 frogs 4.1.0 (0/28) (0/28) (0/28) (28/28) True True