Galaxy wrapper id	Galaxy tool ids	Description	bio.tool id	bio.tool ids	bio.tool name	bio.tool description	EDAM operation	EDAM topic	Status	Source	ToolShed categories	ToolShed id	Galaxy wrapper owner	Galaxy wrapper source	Galaxy wrapper parsed folder	Galaxy wrapper version	Conda id	Conda version	EDAM operation (no superclasses)	EDAM topic (no superclasses)	Available on UseGalaxy.org (Main)	Available on UseGalaxy.org.au	Available on UseGalaxy.eu	Available on UseGalaxy.fr	Tools available on UseGalaxy.org (Main)	Tools available on UseGalaxy.org.au	Tools available on UseGalaxy.eu	Tools available on UseGalaxy.fr	Tools available on Galaxy@AuBi	Tools available on Galaxy@Pasteur	Tools available on GalaxyTrakr	Tools available on HyPhy HIV NGS Tools	Tools available on IPK Galaxy Blast Suite	Tools available on MISSISSIPPI	Tools available on PepSimili	Tools available on UseGalaxy.cz	Tools available on UseGalaxy.no	Tools available on Viral Variant Visualizer (VVV)	No. of tool users (2022-2023) (usegalaxy.eu)	Total tool usage (usegalaxy.eu)	Deprecated
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	0	5	5	5	0	0	0	0	0	0	0	5	4	0	73	1004	False
TreeBest	treebest_best	TreeBeST best	treebest	treebest	TreeBeST	TreeBeST, which stands for (gene) Tree Building guided by Species Tree, is a versatile program that builds, manipulates and displays phylogenetic trees. It is particularly designed for building gene trees with a known species tree and is highly efficient and accurate.TreeBeST is previously known as NJTREE. It has been largely used in the TreeFam database, Ensembl Compara and OPTIC database of Chris Ponting group.	Phylogenetic tree visualisation, Phylogenetic analysis, Phylogenetic inference (from molecular sequences)	Phylogenetics	To update	http://treesoft.sourceforge.net/treebest.shtml	Phylogenetics	treebest_best	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest	1.9.2.post0	treebest	1.9.2.post1	Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogenetics	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	1	1	0	23	984	False
abacas	abacas	Order and Orientate Contigs							To update	https://github.com/phac-nml/abacas	Assembly	abacas	nml	https://github.com/phac-nml/abacas	https://github.com/phac-nml/galaxy_tools/tree/master/tools/abacas	1.1	mummer	3.23			0	0	0	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	False
abricate	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	Antimicrobial resistance prediction	Genomics, Microbiology	3	3	3	3	3	3	3	3	3	0	3	0	0	0	0	3	3	0	1764	496717	False
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	Up-to-date	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	1.0.19	abritamr	1.0.19	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	False
abyss	abyss-pe	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler	abyss	abyss	ABySS	De novo genome sequence assembler using short reads.	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	Up-to-date	http://www.bcgsc.ca/platform/bioinfo/software/abyss	Assembly	abyss	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/abyss	https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss	2.3.9	abyss	2.3.9	Genome assembly, De-novo assembly, Scaffolding	Sequence assembly	0	1	1	0	0	1	1	0	0	0	1	0	0	1	0	1	1	0	391	4278	False
aldex2	aldex2	Performs analysis Of differential abundance taking sample variation into account	aldex2	aldex2	ALDEx2	A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction.	Statistical inference	Gene expression, Statistics and probability	To update	https://github.com/ggloor/ALDEx_bioc	Metagenomics	aldex2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2	1.26.0	bioconductor-aldex2	1.34.0	Statistical inference	Gene expression, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	13	129	False
amplican	amplican	AmpliCan is an analysis tool for genome editing.	amplican	amplican	amplican	It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	To update	https://github.com/valenlab/amplican	Sequence Analysis	amplican	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/amplican	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican	1.14.0	bioconductor-amplican	1.24.0	Alignment, Standardisation and normalisation	PCR experiment, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	12	53	False
amrfinderplus	amrfinderplus	"AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms.	amrfinderplus	amrfinderplus	AMRFinderPlus	AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	Up-to-date	https://github.com/ncbi/amr	Sequence Analysis	AMRFinderPlus	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus	3.12.8	ncbi-amrfinderplus	3.12.8	Antimicrobial resistance prediction	Microbiology, Public health and epidemiology, Infectious disease	1	0	1	1	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	591	False
ancombc	ancombc	Performs analysis of compositions of microbiomes with bias correction.	ancombc	ancombc	ANCOMBC	Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment.	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	To update	https://github.com/FrederickHuangLin/ANCOMBC	Metagenomics	ancombc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ancombc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc	1.4.0	bioconductor-ancombc	2.4.0	DNA barcoding	Microbial ecology, Metagenomics, Taxonomy	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	4	7	False
antismash	antismash	Antismash allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters	antismash	antismash	antiSMASH	Rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	To update	https://antismash.secondarymetabolites.org	Sequence Analysis	antismash	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash	https://github.com/bgruening/galaxytools/tree/master/tools/antismash	6.1.1	antismash	7.1.0	Sequence clustering, Gene prediction, Differential gene expression analysis	Molecular interactions, pathways and networks, Gene and protein families	1	1	1	0	1	1	1	0	0	0	1	0	0	0	0	1	1	0	279	14596	False
artic	artic_guppyplex, artic_minion	The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building	artic	artic	ARTIC	A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore	Sequence alignment	Genomics	To update	https://github.com/artic-network/fieldbioinformatics	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/artic	https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic		artic	1.2.4	Sequence alignment	Genomics	0	2	2	0	0	2	2	0	0	0	1	0	0	0	0	2	1	0	123	8175	False
assemblystats	assemblystats	Summarise an assembly (e.g. N50 metrics)							To update	https://github.com/phac-nml/galaxy_tools	Assembly	assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/assemblystats	1.1.0	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	False
bakta	bakta	"Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis."	bakta	bakta	Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	Up-to-date	https://github.com/oschwengers/bakta	Sequence Analysis	bakta	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta	1.9.4	bakta	1.9.4	Genome annotation	Genomics, Data submission, annotation and curation, Sequence analysis	1	1	1	1	1	1	1	1	1	0	1	0	0	0	0	1	1	0	151	2982	False
bamtools	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	Data handling, Sequence alignment analysis	Sequencing, Sequence analysis	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	1	1	0	208	14021	False
bandage	bandage_image, bandage_info	Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily	bandage	bandage	Bandage	GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms.	Sequence assembly visualisation	Genomics, Sequence assembly	Up-to-date	https://github.com/rrwick/Bandage	Visualization	bandage	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage	2022.09	bandage_ng	2022.09	Sequence assembly visualisation	Genomics, Sequence assembly	2	2	2	2	2	2	2	2	2	2	2	0	0	2	0	2	2	0	2016	44390	False
bayescan	BayeScan	Detecting natural selection from population-based genetic data	bayescan	bayescan	BayeScan	BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model.	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	To update	http://cmpg.unibe.ch/software/BayeScan/index.html	Sequence Analysis	bayescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bayescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan	2.1	bayescan	2.0.1	Statistical inference	Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	8	64	False
bbtools	bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole	BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.	bbmap	bbmap, bbtools	BBMap	BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	Up-to-date	https://jgi.doe.gov/data-and-tools/bbtools/	Sequence Analysis	bbtools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools	39.08	bbmap	39.08	RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment	RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq	6	3	5	0	6	3	5	0	0	0	3	1	0	0	0	4	0	0	420	6381	False
bigscape	bigscape	Construct sequence similarity networks of BGCs and groups them into GCF	BiG-SCAPE	BiG-SCAPE	BiG-SCAPE	A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	Up-to-date	https://github.com/medema-group/BiG-SCAPE	Metagenomics	bigscape	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape	1.1.9	bigscape	1.1.9	Clustering, Global alignment, Fold recognition	Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	False
binning_refiner	bin_refiner	Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels.	binning_refiner	binning_refiner	Binning_refiner	Improving genome bins through the combination of different binning programs	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	Up-to-date	https://github.com/songweizhi/Binning_refiner	Metagenomics	binning_refiner	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/binning_refiner/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner	1.4.3	binning_refiner	1.4.3	Read binning, Sequence clustering	Metagenomics, Sequence assembly, Microbial ecology	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	1	0	0	21	81	False
biohansel	biohansel	Heidelberg and Enteritidis SNP Elucidation							To update	https://github.com/phac-nml/biohansel	Sequence Analysis	biohansel	nml	https://github.com/phac-nml/biohansel	https://github.com/phac-nml/galaxy_tools/tree/master/tools/biohansel	2.4.0	bio_hansel	2.6.1			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
biom_format	biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table	The biom-format package provides a command line interface and Python API for working with BIOM files.	biomformat	biomformat	biomformat	This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.	Formatting	Laboratory information management, Sequence analysis	To update	https://github.com/biocore/biom-format	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format	https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format	2.1.15	biom-format	2.1.7	Formatting	Laboratory information management, Sequence analysis	2	2	6	0	2	2	6	0	0	1	0	0	0	0	0	1	1	0	98	3906	False
biotradis	bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites	Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data.	biotradis	biotradis	biotradis	The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.	Sequence analysis	Mobile genetic elements, Workflows	Up-to-date	https://www.sanger.ac.uk/science/tools/bio-tradis	Genome annotation	biotradis	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis	https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis	1.4.5	biotradis	1.4.5	Sequence analysis	Mobile genetic elements, Workflows	3	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
blast2go	blast2go	Maps BLAST results to GO annotation terms							To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	Ontology Manipulation, Sequence Analysis	blast2go	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast2go	0.0.11	b2g4pipe				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	101	1232	False
blast_rbh	blast_reciprocal_best_hits	BLAST Reciprocal Best Hits (RBH) from two FASTA files							To update	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	Fasta Manipulation, Sequence Analysis	blast_rbh	peterjc	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh	0.3.0	biopython	1.70			0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	1	1	0	121	22499	False
blastxml_to_top_descr	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	0	1	0	0	0	1	0	0	1	0	0	0	0	0	1	1	0	159	264558	False
bracken	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	3.0	bracken	3.0	Statistical calculation	Metagenomics, Microbial ecology	1	1	1	1	1	1	1	1	1	0	1	0	0	0	0	1	1	0	326	18351	False
busco	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	Up-to-date	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	5.7.1	busco	5.7.1	Sequence assembly validation, Scaffolding, Genome assembly, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	1	1	0	0	0	1	1	0	1804	86180	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	Taxonomic classification, Sequence assembly, Coding region prediction	Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly	5	2	5	0	5	2	5	0	0	0	5	0	0	0	0	5	5	0	268	2878	False
cd_hit_dup	cd_hit_dup	simple tool for removing duplicates from sequencing reads							To update		Metagenomics, Sequence Analysis	cd_hit_dup	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tools/cd_hit_dup	https://github.com/galaxyproject/tools-devteam/tree/main/tools/cd_hit_dup	0.0.1	cd-hit-auxtools	4.8.1			1	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	False
cdhit	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	Sequence clustering	Sequencing	0	0	1	1	0	0	1	1	1	0	0	0	0	0	0	1	1	0	280	4474	False
cemitool	cemitool	Gene co-expression network analysis tool	cemitool	cemitool	CEMiTool	It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.	Enrichment analysis, Pathway or network analysis	Gene expression, Transcriptomics, Microarray experiment	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html	Transcriptomics, RNA, Statistics	cemitool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cemitool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool	1.26.0	bioconductor-cemitool	1.26.0	Enrichment analysis, Pathway or network analysis	Transcriptomics, Microarray experiment	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	0	9	98	False
checkm	checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes	checkm	checkm	CheckM	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.	Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation	Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	Up-to-date	https://github.com/Ecogenomics/CheckM	Metagenomics	checkm	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm	1.2.3	checkm-genome	1.2.3	Sequence assembly validation, Sequence composition calculation, Statistical calculation	Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management	0	0	10	10	0	0	10	10	0	0	10	0	0	0	0	10	0	0	390	5165	False
clair3	clair3	Symphonizing pileup and full-alignment for high-performance long-read variant calling	clair3	clair3	Clair3	Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.	Variant calling	Molecular genetics	To update	https://github.com/HKU-BAL/Clair3	Sequence Analysis, Variant Analysis	clair3	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3	1.0.8	clair3	1.0.10	Variant calling	Molecular genetics	0	1	1	0	0	1	1	0	0	0	1	0	0	0	0	1	0	0	68	1856	False
clinod	clinod	NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins	clinod	clinod	clinod	The command line NoD predictor (clinod) can be run from the command line to predict Nucleolar localization sequences (NoLSs) that are short targeting sequences responsible for the localization of proteins to the nucleolus.The predictor accepts a list of FASTA formatted sequences as an input and outputs the NOLS predictions as a result.Please note that currently, JPred secondary structure predictions are not supported by clinod. However, we are working on it.	Nucleic acid sequence analysis	Sequence analysis	To update	http://www.compbio.dundee.ac.uk/www-nod/	Sequence Analysis	clinod	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	https://github.com/peterjc/pico_galaxy/tree/master/tools/clinod	0.1.0	clinod	1.3	Nucleic acid sequence analysis	Sequence analysis	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
clustalw	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	Multiple sequence alignment	Phylogeny, Sequence analysis	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	1	0	651	46793	False
cmsearch_deoverlap	cmsearch_deoverlap	removes lower scoring overlaps from cmsearch results.	cmsearch-deoverlap	cmsearch-deoverlap	cmsearch-deoverlap	Removes lower scoring overlaps from cmsearch results.	Comparison, Alignment	Biology, Medicine	To update	https://github.com/EBI-Metagenomics/pipeline-v5/blob/master/tools/RNA_prediction/cmsearch-deoverlap/cmsearch-deoverlap.pl	RNA	cmsearch_deoverlap	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap	0.08+galaxy2	perl		Comparison, Alignment	Biology, Medicine	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	1	102	False
codeml	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	Probabilistic sequence generation	Phylogenetics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	29	60901	False
cojac	cooc_mutbamscan, cooc_pubmut, cooc_tabmut	co-occurrence of mutations on amplicons	cojac	cojac	COJAC	CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag.		Genetic variation	Up-to-date	https://github.com/cbg-ethz/cojac	Metagenomics, Sequence Analysis	cojac	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac	0.9.2	cojac	0.9.2		Genetic variation	2	0	3	0	2	0	3	0	0	0	0	0	0	0	0	3	0	0	20	2757	False
combine_assembly_stats	combine_stats	Combine multiple Assemblystats datasets into a single tabular report							To update	https://github.com/phac-nml/galaxy_tools	Assembly	combine_assemblystats	nml	https://github.com/phac-nml/galaxy_tools	https://github.com/phac-nml/galaxy_tools/tree/master/tools/combine_assembly_stats	1.0	perl-getopt-long	2.58			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
combine_metaphlan_humann	combine_metaphlan_humann	Combine MetaPhlAn2 and HUMAnN2 outputs to relate genus/species abundances and gene families/pathways abundances	combine_metaphlan_and_humann	combine_metaphlan_and_humann	Combine Metaphlan and HUMAnN	This tool combine MetaPhlAn outputs and HUMANnN outputs	Aggregation	Metagenomics, Molecular interactions, pathways and networks	To update		Metagenomics	combine_metaphlan2_humann2	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2	https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan_humann	0.3.0	python		Aggregation	Metagenomics, Molecular interactions, pathways and networks	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	0	9	147	False
compare_humann2_output	compare_humann2_output	Compare outputs of HUMAnN2 for several samples and extract similar and specific information	compare_humann2_outputs	compare_humann2_outputs	Compare HUMAnN2 outputs	This tool compare HUMANnN2 outputs with gene families or pathways and their relative abundances between several samples	Comparison	Metagenomics, Gene and protein families	To update		Metagenomics	compare_humann2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	https://github.com/bgruening/galaxytools/tree/master/tools/compare_humann2_output	0.2.0			Comparison	Metagenomics, Gene and protein families	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	10	332	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	Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly	Sequence assembly, Transcriptomics, Sequence analysis	1	1	1	1	1	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	False
concoct	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	Sequence clustering, Read binning	Metagenomics	0	0	5	5	0	0	5	5	0	0	0	0	0	0	0	5	0	0	92	786	False
coverm	coverm_contig, coverm_genome	CoverM genome and contig wrappers	coverm	coverm	CoverM	Read coverage calculator for metagenomics	Local alignment	Bioinformatics	Up-to-date	https://github.com/wwood/CoverM	Sequence Analysis	coverm	iuc	https://github.com/galaxyproject/tools-iuc/tools/coverm	https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm	0.7.0	coverm	0.7.0	Local alignment	Bioinformatics	0	0	2	2	0	0	2	2	0	0	2	0	0	0	0	2	0	0	72	529	False
cryptogenotyper	CryptoGenotyper	CryptoGenotyper is a standalone tool to in-silico determine species and subtype based on SSU rRNA and gp60 markers.							Up-to-date	https://github.com/phac-nml/CryptoGenotyper	Sequence Analysis	cryptogenotyper	nml	https://github.com/phac-nml/CryptoGenotyper	https://github.com/phac-nml/galaxy_tools/tree/master/tools/cryptogenotyper	1.0	cryptogenotyper	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	16	8518	False
cutadapt	cutadapt	Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq).	cutadapt	cutadapt	Cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	Up-to-date	https://cutadapt.readthedocs.org/en/stable/	Fasta Manipulation, Fastq Manipulation, Sequence Analysis	cutadapt	lparsons	https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt	https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt	4.9	cutadapt	4.9	Sequence trimming, Primer removal, Read pre-processing	Genomics, Probes and primers, Sequencing	1	1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	1	0	5090	232004	False
dada2	dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_removeBimeraDenovo, dada2_seqCounts	DADA2 wrappers	dada2	dada2	dada2	This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier.	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	To update	https://benjjneb.github.io/dada2/index.html	Metagenomics	dada2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2		bioconductor-dada2	1.30.0	Variant calling, DNA barcoding	Sequencing, Genetic variation, Microbial ecology, Metagenomics	10	10	10	10	10	10	10	10	10	0	10	1	0	0	0	10	10	0	1263	66609	False
das_tool	Fasta_to_Contig2Bin, das_tool	DAS Tool for genome resolved metagenomics	dastool	dastool	dastool	DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.	Read binning	Metagenomics	Up-to-date	https://github.com/cmks/DAS_Tool	Metagenomics	das_tool	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool	https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool	1.1.7	das_tool	1.1.7	Read binning	Metagenomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	2	0	0	24	706	False
deseq2	deseq2	Differential gene expression analysis based on the negative binomial distribution	DESeq2	DESeq2	DESeq2	R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	To update	https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html	Transcriptomics, RNA, Statistics	deseq2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2	2.11.40.8	bioconductor-deseq2	1.42.0	Differential gene expression analysis, RNA-Seq analysis	RNA-Seq	1	1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	1	0	4990	95752	False
diamond	bg_diamond, bg_diamond_makedb, bg_diamond_view	DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.	diamond	diamond	Diamond	Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.	Sequence alignment analysis	Sequence analysis, Proteins	To update	https://github.com/bbuchfink/diamond	Sequence Analysis	diamond	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond	https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond	2.0.15	diamond	2.1.9	Sequence alignment analysis	Sequence analysis, Proteins	3	3	3	3	3	3	3	3	3	3	3	0	1	0	0	3	3	0	963	49711	False
disco	disco	DISCO is a overlap-layout-consensus (OLC) metagenome assembler	disco	disco	DISCO	DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer.	Protein sequence analysis	Structure determination	To update	http://disco.omicsbio.org/	Metagenomics, Assembly	disco	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco		disco	1.2	Protein sequence analysis	Structure determination	1	0	1	0	1	0	1	0	0	0	1	0	0	0	0	1	1	0	42	369	False
dram	dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer	DRAM for distilling microbial metabolism to automate the curation of microbiome function	dram	dram	DRAM	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	Up-to-date	https://github.com/WrightonLabCSU/DRAM	Metagenomics	dram	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram	https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram	1.5.0	dram	1.5.0	Gene functional annotation	Metagenomics, Biological databases, Molecular genetics	0	0	5	0	0	0	5	0	0	0	0	0	0	0	0	5	0	0	39	6886	False
drep	drep_compare, drep_dereplicate	dRep compares and dereplicates genome sets	drep	drep	dRep	Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication.	Genome comparison	Metagenomics, Genomics, Sequence analysis	Up-to-date	https://github.com/MrOlm/drep	Metagenomics	drep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep	3.5.0	drep	3.5.0	Genome comparison	Metagenomics, Sequence analysis	0	0	2	2	0	0	2	2	0	0	2	0	0	0	0	2	2	0	46	646	False
ectyper	ectyper	EC-Typer - in silico serotyping of Escherichia coli species							Up-to-date	https://github.com/phac-nml/ecoli_serotyping	Sequence Analysis	ectyper	nml	https://github.com/phac-nml/ecoli_serotyping	https://github.com/phac-nml/galaxy_tools/tree/master/tools/ectyper	1.0.0	ectyper	1.0.0			0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	1	0	0	53	9907	False
effectiveT3	effectiveT3	Find bacterial type III effectors in protein sequences	effectivet3	effectivet3	EffectiveT3	Prediction of putative Type-III secreted proteins.	Sequence classification	Sequence analysis	To update	http://effectors.org	Sequence Analysis	effectivet3	peterjc	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3	0.0.21	effectiveT3	1.0.1	Sequence classification	Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
eggnog_mapper	eggnog_mapper, eggnog_mapper_annotate, eggnog_mapper_search	eggnog-mapper fast functional annotation of novel sequences	eggnog-mapper-v2	eggnog-mapper-v2	eggNOG-mapper v2	EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only.	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	To update		Proteomics	eggnog_mapper	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper	2.1.8	eggnog-mapper	2.1.12	Homology-based gene prediction, Genome annotation, Fold recognition, Information extraction, Query and retrieval	Metagenomics, Phylogeny, Transcriptomics, Workflows, Sequence analysis	3	3	3	3	3	3	3	3	0	0	0	0	0	0	3	3	1	0	510	30565	False
emboss_5	EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110	Galaxy wrappers for EMBOSS version 5.0.0 tools	emboss	emboss	EMBOSS	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis, Biology	To update	http://emboss.open-bio.org/	Sequence Analysis, Fasta Manipulation	emboss_5	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5	https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5	5.0.0	emboss	6.6.0	Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment	Molecular biology, Sequence analysis	107	107	107	107	107	107	107	107	0	0	107	107	0	107	0	107	107	0	1816	89530	False
ete	ete_gene_csv_finder, ete_genetree_splitter, ete_homology_classifier, ete_init_taxdb, ete_lineage_generator, ete3_mod, ete_species_tree_generator	Analyse phylogenetic trees using the ETE Toolkit	ete	ete	ete	The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org	Phylogenetic analysis, Phylogenetic tree editing	Phylogenetics	To update	http://etetoolkit.org/	Phylogenetics	ete	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete	3.1.2	ete3	3.1.1	Phylogenetic tree editing	Phylogenetics	0	0	7	7	0	0	7	7	0	0	0	0	0	0	0	7	7	0	45	899	False
export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn	export2graphlan	export2graphlan	export2graphlan	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important.	Conversion	Taxonomy, Metabolomics, Biomarkers	To update	https://bitbucket.org/CibioCM/export2graphlan/overview	Metagenomics	export2graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/export2graphlan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan	0.20	export2graphlan	0.22	Conversion	Taxonomy, Metabolomics, Biomarkers	1	1	1	1	1	1	1	1	0	0	1	0	0	0	0	1	1	0	200	5265	False
ez_histograms	ez_histograms	ggplot2 histograms and density plots							To update	https://github.com/tidyverse/ggplot2	Visualization, Statistics	ez_histograms	artbio	https://github.com/artbio/tools-artbio/tree/main/tools/ez_histograms	https://github.com/ARTbio/tools-artbio/tree/main/tools/ez_histograms	3.4.4	r-ggplot2	2.2.1			0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	False
fargene	fargene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr )	fargene	fargene	fARGene	fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	Up-to-date	https://github.com/fannyhb/fargene	Sequence Analysis	fargene	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene	0.1	fargene	0.1	Antimicrobial resistance prediction	Metagenomics, Microbiology, Public health and epidemiology	1	0	1	0	1	0	1	0	0	0	1	0	0	0	0	1	1	0	52	459	False
fastani	fastani	Fast alignment-free computation of whole-genome Average Nucleotide Identity	fastani	fastani	FastANI	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	To update	https://github.com/ParBLiSS/FastANI	Sequence Analysis	fastani	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastani	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani	1.3	fastani	1.34	Genome alignment, Sequence similarity search	Microbiology, Genetic variation	0	0	1	1	0	0	1	1	0	0	1	0	0	0	0	1	1	0	250	3498	False
fastk	fastk_fastk	FastK: A K-mer counter (for HQ assembly data sets)							To update	https://github.com/thegenemyers/FASTK	Assembly	fastk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk	1.0.0	fastk	1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	False
fastp	fastp	Fast all-in-one preprocessing for FASTQ files	fastp	fastp	fastp	A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.	Sequencing quality control, Sequence contamination filtering	Sequence analysis, Probes and primers	Up-to-date	https://github.com/OpenGene/fastp	Sequence Analysis	fastp	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp	0.23.4	fastp	0.23.4	Sequence contamination filtering	Probes and primers	1	1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	1	1	2803	1055760	False
fastqe	fastqe	FASTQE	fastqe	fastqe	FASTQE	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.	Sequencing quality control	Sequence analysis, Sequencing	To update	https://fastqe.com/	Sequence Analysis	fastqe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe	0.3.1+galaxy0	fastqe	0.3.1	Sequencing quality control	Sequence analysis, Sequencing	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	1	1	0	1266	4333	False
fasttree	fasttree	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL	fasttree	fasttree	FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.	Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Sequence analysis	To update	http://www.microbesonline.org/fasttree/	Phylogenetics	fasttree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasttree	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree	2.1.10	fasttree	2.1.11		Phylogenetics	1	1	1	1	1	1	1	1	1	1	1	0	0	1	0	1	1	0	379	55434	False
featurecounts	featurecounts	featureCounts counts the number of reads aligned to defined masked regions in a reference genome	featurecounts	featurecounts	FeatureCounts	featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package.	Read summarisation, RNA-Seq quantification	RNA-Seq	To update	http://bioinf.wehi.edu.au/featureCounts	RNA, Transcriptomics, Sequence Analysis	featurecounts	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts	https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts	2.0.3	subread	2.0.6	Read summarisation, RNA-Seq quantification	RNA-Seq	1	1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	1	0	4679	696399	False
filter_spades_repeats	filter_spades_repeat	Remove short and repeat contigs/scaffolds							To update	https://github.com/phac-nml/galaxy_tools/	Assembly	filter_spades_repeats	nml	https://github.com/phac-nml/galaxy_tools/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/filter_spades_repeats	1.0.1	perl-bioperl	1.7.8			0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	False
filtlong	filtlong	Filtlong - Filtering long reads by quality	filtlong	filtlong	Filtlong	Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.	Filtering, Sequencing quality control		Up-to-date	https://github.com/rrwick/Filtlong	Fastq Manipulation, Sequence Analysis	filtlong	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/filtlong	https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong	0.2.1	filtlong	0.2.1	Filtering, Sequencing quality control		1	1	1	1	1	1	1	1	0	1	1	0	0	0	0	1	1	0	617	30483	False
flashlfq	flashlfq	FlashLFQ mass-spectrometry proteomics label-free quantification	flashlfq	flashlfq	FlashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.	Label-free quantification	Proteomics experiment, Proteomics	To update	https://github.com/smith-chem-wisc/FlashLFQ	Proteomics	flashlfq	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/flashlfq	1.0.3.1	flashlfq	1.2.6	Label-free quantification	Proteomics experiment, Proteomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	17	645	False
flye	flye	Assembly of long and error-prone reads.	Flye	Flye	Flye	Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs.	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing, Genomics	Up-to-date	https://github.com/fenderglass/Flye/	Assembly	flye	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/flye	https://github.com/bgruening/galaxytools/tree/master/tools/flye	2.9.5	flye	2.9.5	Genome assembly, De-novo assembly, Mapping assembly, Cross-assembly	Sequence assembly, Metagenomics, Whole genome sequencing	1	1	1	1	1	1	1	1	0	1	1	1	0	0	0	1	1	0	1499	20904	False
format_metaphlan2_output	format_metaphlan2_output	Format MetaPhlAn2 output to extract abundance at different taxonomic levels	format_metaphlan2_output	format_metaphlan2_output	Format metaphlan2 output	This tool format output file of MetaPhlan2 containing community content (abundance) at all taxonomic levels (from kingdom to strains).	Formatting	Taxonomy, Metagenomics	To update		Metagenomics	format_metaphlan2_output	bebatut	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output/	https://github.com/bgruening/galaxytools/tree/master/tools/format_metaphlan2_output	0.2.0			Formatting	Taxonomy, Metagenomics	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	1	1	0	166	5588	False
fraggenescan	fraggenescan	Tool for finding (fragmented) genes in short read	fraggenescan	fraggenescan	FragGeneScan	Application for finding (fragmented) genes in short reads	Gene prediction	Genetics, Sequence analysis	To update	https://sourceforge.net/projects/fraggenescan/	Sequence Analysis	fraggenescan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/fraggenescan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan		fraggenescan	1.31	Gene prediction	Genetics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	1	0	0	0	0	1	1	0	68	1102	False
freyja	freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants	lineage abundances estimation	freyja	freyja	Freyja	Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset	RNA-Seq quantification	Metagenomics	To update	https://github.com/andersen-lab/Freyja	Metagenomics, Sequence Analysis	freyja	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja	https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja	1.4.4	freyja	1.5.1	RNA-Seq quantification	Metagenomics	2	0	4	0	2	0	4	0	0	0	4	0	0	0	0	4	0	0	55	20021	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	frogs	frogs	FROGS	The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	To update	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	5.0.0	Taxonomic classification	Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing	0	0	0	28	0	0	0	28	0	18	18	0	0	0	0	0	0	0	0	0	False
funannotate	funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort	Funannotate is a genome prediction, annotation, and comparison software package.	funannotate	funannotate	funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).	Genome annotation	Genomics	To update	https://funannotate.readthedocs.io	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate	1.8.15			Genome annotation	Genomics	3	5	5	5	3	5	5	5	0	0	0	0	0	0	0	5	0	0	900	5906	False
getmlst	getmlst	Download MLST datasets by species from pubmlst.org							To update		Sequence Analysis	getmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/getmlst	0.1.4.1	srst2	0.2.0			0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	False
ggplot2	ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details.	ggplot2	ggplot2	ggplot2	Plotting system for R, based on the grammar of graphics.	Visualisation	Data visualisation	To update	https://github.com/tidyverse/ggplot2	Visualization		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2	3.4.0	r-base		Visualisation	Data visualisation	5	5	5	5	5	5	5	5	1	0	5	0	0	3	0	5	5	0	1388	22148	False
gi2taxonomy	Fetch Taxonomic Ranks	Fetch taxonomic representation	gi2taxonomy	gi2taxonomy	gi2taxonomy	The tool fetches taxonomic information for a list of sequence identifiers (i.e. GI numbers, as used by the National Center for Biotechnology Information (NCBI).	Database search, ID mapping	Taxonomy	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	gi2taxonomy	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/gi2taxonomy	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/gi2taxonomy	1.1.1	taxonomy	0.10.0	Database search, ID mapping	Taxonomy	0	0	1	0	0	0	1	0	0	1	1	0	0	0	0	1	0	0	27	660	False
glimmer	glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based	Glimmer makes gene predictions.	gemini	gemini	GEMINI	GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics.	Sequence analysis, Genetic variation analysis	Sequence analysis	To update	https://ccb.jhu.edu/software/glimmer/	Sequence Analysis		bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer		glimmer	3.02	Sequence analysis, Genetic variation analysis	Sequence analysis	0	0	4	0	0	0	4	0	0	0	0	0	0	0	0	4	0	0	187	3965	False
glimmer_hmm		GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM)							To update	https://ccb.jhu.edu/software/glimmerhmm/	Sequence Analysis	glimmer_hmm	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm	https://github.com/bgruening/galaxytools/tree/master/tools/glimmer_hmm						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
goenrichment	goenrichment, goslimmer	Performs GO Enrichment analysis.	goenrichment	goenrichment	GOEnrichment	GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência.	Gene-set enrichment analysis	Transcriptomics	Up-to-date	https://github.com/DanFaria/GOEnrichment	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment	2.0.1	goenrichment	2.0.1	Gene-set enrichment analysis	Transcriptomics	2	2	2	2	2	2	2	2	0	0	2	0	0	0	0	2	2	0	408	5484	False
goseq	goseq	goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data	goseq	goseq	GOseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.	Gene functional annotation	RNA-Seq	To update	https://bioconductor.org/packages/release/bioc/html/goseq.html	Statistics, RNA, Micro-array Analysis	goseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq	1.50.0	bioconductor-goseq	1.54.0	Gene functional annotation	RNA-Seq	1	1	1	1	1	1	1	1	1	0	0	1	0	1	0	1	1	0	1210	19167	False
graphlan	graphlan, graphlan_annotate	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees	graphlan	graphlan	GraPhlAn	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	To update	https://github.com/biobakery/graphlan	Metagenomics, Graphics, Phylogenetics	graphlan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan		graphlan	1.1.3	Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification	Metagenomics, Phylogenetics, Phylogenomics, Cladistics	2	2	2	2	2	2	2	2	0	0	2	0	0	0	0	2	2	0	432	9277	False
graphmap	graphmap_align, graphmap_overlap	Mapper for long, error-prone reads.	graphmap	graphmap	graphmap	Splice-aware RNA-seq mapper for long reads \| GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	To update	https://github.com/isovic/graphmap/	Assembly	graphmap	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	https://github.com/bgruening/galaxytools/tree/master/tools/graphmap	0.5.2	graphmap	0.6.4	Sequence trimming, EST assembly, Read mapping	Gene transcripts, RNA-Seq, RNA splicing	0	0	2	0	0	0	2	0	0	0	2	0	0	0	0	2	2	0	136	6651	False
gtdbtk	gtdbtk_classify_wf	GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes.	GTDB-Tk	GTDB-Tk	GTDB-Tk	a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3).	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	To update	https://github.com/Ecogenomics/GTDBTk	Metagenomics	gtdbtk	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtdbtk	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk	2.3.2	gtdbtk	2.4.0	Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval	Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins	0	1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	False
gubbins	gubbins	Gubbins - bacterial recombination detection	gubbins	gubbins	Gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	To update		Sequence Analysis	gubbins	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins	https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins	3.2.1	gubbins	3.3.5	Genotyping, Phylogenetic inference, Ancestral reconstruction	Phylogeny, Genotype and phenotype, Whole genome sequencing	1	1	1	0	1	1	1	0	0	0	1	0	0	0	0	1	1	0	145	3340	False
hamronization	hamronize_summarize, hamronize_tool	Convert AMR gene detection tool output to hAMRonization specification format.	hamronization	hamronization	hAMRonization	Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure	Data handling, Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	Up-to-date	https://github.com/pha4ge/hAMRonization	Sequence Analysis	hamronization	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization	1.1.4	hamronization	1.1.4	Antimicrobial resistance prediction, Parsing	Public health and epidemiology, Microbiology, Bioinformatics	0	0	2	2	0	0	2	2	0	0	2	0	0	0	0	2	0	0	117	4459	False
hansel	bio_hansel	Heidelberg and Enteritidis SNP Elucidation	Biohansel	Biohansel	BioHansel	BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile.	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	Up-to-date	https://github.com/phac-nml/bio_hansel	Sequence Analysis	bio_hansel	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel	2.6.1	bio_hansel	2.6.1	Genotyping, SNP detection, Genome assembly	Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	18	339	False
hifiasm_meta	hifiasm_meta	A hifiasm fork for metagenome assembly using Hifi reads.	hifiasm-meta	hifiasm-meta	Hifiasm-meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.	Sequence assembly	Sequence assembly, Metagenomics	To update	https://github.com/xfengnefx/hifiasm-meta	Metagenomics	hifiasm_meta	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hifiasm_meta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta	0.3.1	hifiasm_meta	hamtv0.3.1	Sequence assembly	Sequence assembly, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	1	0	0	12	137	False
hivtrace	hivtrace	An application that identifies potential transmission clusters within a supplied FASTA file with an option to find potential links against the Los Alamos HIV Sequence Database.							To update		Sequence Analysis	hivtrace	nml	https://github.com/phac-nml/galaxy_tools/tree/tools/hivtrace	https://github.com/phac-nml/galaxy_tools/tree/master/tools/hivtrace	1.0.1	hivtrace	1.5.0			0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	False
hmmer3	hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer	HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs).	hmmer3	hmmer3	HMMER3	This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	Up-to-date	http://hmmer.org/	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3	3.4	hmmer	3.4	Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search	Sequence analysis, Sequence sites, features and motifs, Gene and protein families	0	12	12	12	0	12	12	12	0	0	12	0	0	0	0	12	12	0	439	33702	False
humann	humann, humann_associate, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_rna_dna_norm, humann_split_stratified_table, humann_split_table, humann_strain_profiler, humann_unpack_pathways	HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution	humann	humann	humann	HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	To update	http://huttenhower.sph.harvard.edu/humann	Metagenomics	humann	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann	https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann	3.8	humann	3.9	Species frequency estimation, Taxonomic classification, Phylogenetic analysis	Metagenomics, Phylogenomics	6	13	13	13	6	13	13	13	0	0	13	0	0	0	0	13	13	0	1045	19521	False
hyphy	hyphy_absrel, hyphy_annotate, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs, hyphy_summary	Hypothesis Testing using Phylogenies	HyPhy	HyPhy	HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	To update	http://www.hyphy.org	Phylogenetics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy	2.5.47	hyphy	2.5.62	Statistical calculation	Phylogeny, Small molecules, Molecular interactions, pathways and networks	17	2	17	2	17	2	17	2	0	0	0	0	0	2	0	17	12	0	161	10370	False
hypo	hypo	Super Fast & Accurate Polisher for Long Read Genome Assemblies	HyPo	HyPo	HyPo	HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes.	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	Up-to-date	https://github.com/kensung-lab/hypo	Assembly	hypo	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/hypo	https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo	1.0.3	hypo	1.0.3	Optimisation and refinement, Genome assembly	Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	39	354	False
icescreen	icescreen	ICEscreen identifies Integrative Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) in Bacillota genomes.	icescreen	icescreen	ICEscreen	A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures.	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	To update	https://icescreen.migale.inrae.fr/	Genome annotation	icescreen	iuc	https://forgemia.inra.fr/ices_imes_analysis/icescreen	https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen	1.3.1	icescreen	1.3.2	Database search, Protein feature detection	Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	False
idba_ud	idba_hybrid, idba_tran, idba_ud	Wrappers for the idba assembler variants.	idba	idba	IDBA	A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system.	Sequence assembly	Sequence assembly	To update	https://i.cs.hku.hk/~alse/hkubrg/projects/index.html	Assembly	idba	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/idba_ud	https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud		idba	1.1.3	Sequence assembly	Sequence assembly	3	0	3	3	3	0	3	3	0	0	0	0	0	0	0	3	3	0	69	1127	False
infernal	infernal_cmalign, infernal_cmbuild, infernal_cmpress, infernal_cmscan, infernal_cmsearch, infernal_cmstat	Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.	infernal	infernal	Infernal	Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	To update	http://infernal.janelia.org/	RNA	infernal	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/infernal	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/infernal	1.1.4	infernal	1.1.5	Nucleic acid feature detection	Sequence sites, features and motifs, Structural genomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	6	6	0	67	100294	False
instrain	instrain_compare, instrain_profile	InStrain is a tool for analysis of co-occurring genome populations from metagenomes	instrain	instrain	InStrain	InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification	SNP detection, Genome comparison	Mapping, Metagenomics	To update	https://instrain.readthedocs.io/en/latest/#	Metagenomics	instrain	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/instrain	https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain	1.5.3	instrain	1.9.0	SNP detection, Genome comparison	Mapping, Metagenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	2	0	0	5	94	False
integron_finder	integron_finder	"IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching"	integron_finder	integron_finder	Integron Finder	A tool to detect Integron in DNA sequences.	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	Up-to-date	https://github.com/gem-pasteur/Integron_Finder	Sequence Analysis	integronfinder	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/integron_finder	https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder	2.0.5	integron_finder	2.0.5	Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation	Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	58	52965	False
interproscan	interproscan	Interproscan queries the interpro database and provides annotations.	interproscan_ebi	interproscan_ebi	InterProScan (EBI)	Scan sequences against the InterPro protein signature databases.	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	interproscan	bgruening	https://github.com/galaxyproject/tools-iuc/tree/master/tools/interproscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan	5.59-91.0	interproscan	5.59_91.0	Sequence motif recognition, Protein feature detection	Gene and protein families, Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	1	1	0	677	35243	False
iprscan5		Interproscan queries the interpro database and provides annotations.							To update	http://www.ebi.ac.uk/Tools/pfa/iprscan5/	Sequence Analysis	iprscan5	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5	https://github.com/bgruening/galaxytools/tree/master/tools/iprscan5						0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
iqtree	iqtree	Efficient phylogenomic software by maximum likelihood	iqtree	iqtree	iqtree	A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time	Phylogenetic analysis, Sequence analysis	Phylogenetics	Up-to-date	http://www.iqtree.org/	Phylogenetics	iqtree	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree	2.3.6	iqtree	2.3.6	Phylogenetic analysis, Sequence analysis	Phylogenetics	1	1	1	0	1	1	1	0	1	0	1	1	0	0	0	1	1	0	681	21598	False
isescan	isescan	"ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements."	ISEScan	ISEScan	ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.	Structural variation detection	Genomics, DNA structural variation, Sequence analysis, Genetic variation	To update	https://github.com/xiezhq/ISEScan	Sequence Analysis	ISEScan	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan	1.7.2.3	isescan	1.7.2.1	Structural variation detection	Genomics, Sequence analysis, Genetic variation	1	1	1	1	1	1	1	1	1	0	1	0	0	0	0	1	0	0	50	57581	False
itsx	itsx	ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences.	ITSx	ITSx	ITSx	TSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	Up-to-date	https://microbiology.se/software/itsx/	Metagenomics	itsx	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	https://github.com/bgruening/galaxytools/tree/master/tools/itsx	1.1.3	itsx	1.1.3	Sequence feature detection	Functional, regulatory and non-coding RNA, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	38	868	False
ivar	ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing							Up-to-date	https://github.com/andersen-lab/ivar	Sequence Analysis	ivar	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar	1.4.3	ivar	1.4.3			5	5	5	5	5	5	5	5	0	0	5	4	0	4	0	5	5	0	1171	1224275	False
jbrowse	jbrowse_to_standalone, jbrowse	JBrowse Genome Browser integrated as a Galaxy Tool	jbrowse	jbrowse	JBrowse	Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse.	Genome visualisation	Genomics	Up-to-date	https://jbrowse.org	Sequence Analysis	jbrowse	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse	1.16.11	jbrowse	1.16.11	Genome visualisation	Genomics	2	2	2	2	2	2	2	2	2	2	2	0	0	2	0	2	2	0	2346	18229	False
jellyfish	jellyfish	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA	Jellyfish	Jellyfish	Jellyfish	A command-line algorithm for counting k-mers in DNA sequence.	k-mer counting	Sequence analysis, Genomics	To update	https://github.com/gmarcais/Jellyfish	Assembly	jellyfish	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish	https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish		kmer-jellyfish	2.3.1	k-mer counting	Sequence analysis, Genomics	0	1	1	1	0	1	1	1	0	0	1	0	0	0	0	1	1	0	91	1138	False
kat_filter	kat_@EXECUTABLE@	Filtering kmers or reads from a database of kmers hashes							To update		Sequence Analysis	kat_filter	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/kat_filter	2.3	kat	2.4.2			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
kc-align	kc-align	Kc-Align custom tool	kc-align	kc-align	kc-align	A fast and accurate tool for performing codon-aware multiple sequence alignments	Multiple sequence alignment	Mapping	Up-to-date	https://github.com/davebx/kc-align	Sequence Analysis	kc_align	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kc-align	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align	1.0.2	kcalign	1.0.2	Multiple sequence alignment	Mapping	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	19	363	False
khmer	khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median	In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more	khmer	khmer	khmer	khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.	Standardisation and normalisation, De-novo assembly	Sequence assembly	Up-to-date	https://khmer.readthedocs.org/	Assembly, Next Gen Mappers	khmer	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/khmer	https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer	3.0.0a3	khmer	3.0.0a3	Standardisation and normalisation, De-novo assembly	Sequence assembly	8	8	8	0	8	8	8	0	0	1	1	0	0	1	0	8	8	0	63	2022	False
kleborate	kleborate	Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC)	kleborate	kleborate	Kleborate	Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020).	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	To update	https://github.com/katholt/Kleborate/wiki	Metagenomics	kleborate	iuc	https://github.com/katholt/Kleborate	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate	2.3.2	kleborate	3.0.9	Multilocus sequence typing, Genome assembly, Virulence prediction	Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	1	0	0	38	319	False
kofamscan	kofamscan	Gene function annotation tool based on KEGG Orthology and hidden Markov model	kofamscan	kofamscan	kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.	Sequence analysis, Gene functional annotation	Genomics	Up-to-date	https://github.com/takaram/kofam_scan	Sequence Analysis	kofamscan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan	1.3.0	kofamscan	1.3.0	Sequence analysis, Gene functional annotation	Genomics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	1	0	0	33	594	False
kraken	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	Taxonomic classification	Taxonomy, Metagenomics	5	5	5	5	5	5	5	5	1	0	0	0	0	0	2	5	5	0	1209	33778	False
kraken2	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	Up-to-date	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	2.1.3	kraken2	2.1.3	Taxonomic classification	Taxonomy, Metagenomics	1	1	1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	0	2367	185308	False
kraken2tax	Kraken2Tax	Convert Kraken output to Galaxy taxonomy data.							To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	kraken2tax	devteam	https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/taxonomy/kraken2tax/	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/kraken2tax	1.2+galaxy0	gawk				1	1	1	0	1	1	1	0	1	0	1	1	0	0	0	1	1	0	481	14683	False
kraken_biom	kraken_biom	Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/)							Up-to-date	https://github.com/smdabdoub/kraken-biom	Metagenomics	kraken_biom	iuc	https://github.com/smdabdoub/kraken-biom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom	1.2.0	kraken-biom	1.2.0			0	1	1	1	0	1	1	1	1	0	0	0	0	0	0	1	1	0	182	1444	False
kraken_taxonomy_report	kraken_taxonomy_report	Kraken taxonomy report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report	Kraken-Taxonomy-Report	view report of classification for multiple samples	Visualisation, Classification	Metagenomics, Taxonomy	To update	https://github.com/blankenberg/Kraken-Taxonomy-Report	Metagenomics	kraken_taxonomy_report	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/kraken_taxonomy_report	https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report	0.0.3	biopython	1.70	Visualisation, Classification	Metagenomics, Taxonomy	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	1	0	354	2527	False
krakentools	krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa	KrakenTools is a suite of scripts to be used alongside the Kraken	krakentools	krakentools	KrakenTools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files	Visualisation, Aggregation	Taxonomy, Metagenomics	Up-to-date	https://github.com/jenniferlu717/KrakenTools	Metagenomics	krakentools	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krakentools	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools	1.2	krakentools	1.2	Visualisation, Aggregation	Taxonomy, Metagenomics	6	6	6	6	6	6	6	6	1	6	6	0	0	0	0	6	0	0	703	16525	False
krocus	krocus	Predict MLST directly from uncorrected long reads	krocus	krocus	krocus	Predict MLST directly from uncorrected long reads	Multilocus sequence typing, k-mer counting	Public health and epidemiology	To update	https://github.com/quadram-institute-bioscience/krocus	Sequence Analysis	krocus	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus	https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus	1.0.1	krocus	1.0.3	Multilocus sequence typing, k-mer counting	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	False
lca_wrapper	lca1	Find lowest diagnostic rank							To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	lca_wrapper	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/lca_wrapper	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/lca_wrapper	1.0.1	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	2	137	False
legsta	legsta	Performs in silico Legionella pneumophila sequence based typing.	legsta	legsta	legsta	Performs in silico Legionella pneumophila sequence based typing	Sequence analysis	Public health and epidemiology	Up-to-date	https://github.com/tseemann/legsta	Sequence Analysis	legsta	iuc	https://github.com/tseemann/legsta	https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta	0.5.1	legsta	0.5.1	Sequence analysis	Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	7	55	False
lighter	lighter	Lighter is a kmer-based error correction method for whole genome sequencing data	lighter	lighter	Lighter	Kmer-based error correction method for whole genome sequencing data. Lighter uses sampling (rather than counting) to obtain a set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Sequencing, Whole genome sequencing, DNA, Genomics	To update	https://github.com/mourisl/Lighter	Sequence Analysis, Fasta Manipulation	lighter	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	https://github.com/bgruening/galaxytools/tree/master/tools/lighter	1.0	lighter	1.1.3	k-mer counting, Sequence read processing, Sequencing quality control, Sequencing error detection	Whole genome sequencing, DNA, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	9	152	False
limma_voom	limma_voom	Perform RNA-Seq differential expression analysis using limma voom pipeline	limma	limma	limma	Data analysis, linear models and differential expression for microarray data.	RNA-Seq analysis	Molecular biology, Genetics	Up-to-date	http://bioconductor.org/packages/release/bioc/html/limma.html	Transcriptomics, RNA, Statistics	limma_voom	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom	https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom	3.58.1	bioconductor-limma	3.58.1	RNA-Seq analysis	Molecular biology, Genetics	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	1	1	0	1012	20344	False
lineagespot	lineagespot	Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s)	lineagespot	lineagespot	lineagespot	Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).	Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	To update	https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html	Metagenomics, Sequence Analysis	lineagespot	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/lineagespot	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot	1.6.0	r-base		Variant calling	Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	2	37	False
lorikeet	lorikeet_spoligotype	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	lorikeet	lorikeet	lorikeet	Tools for M. tuberculosis DNA fingerprinting (spoligotyping)	Sequence analysis, Genotyping	Genotype and phenotype	Up-to-date	https://github.com/AbeelLab/lorikeet	Sequence Analysis	lorikeet_spoligotype	iuc	https://github.com/AbeelLab/lorikeet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet	20	lorikeet	20	Sequence analysis, Genotyping	Genotype and phenotype	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	9	647	False
lotus2	lotus2	LotuS2 OTU processing pipeline	lotus2	lotus2	lotus2	LotuS2 is a lightweight and user-friendly pipeline that is fast, precise, and streamlined, using extensive pre- and post-ASV/OTU clustering steps to further increase data quality. High data usage rates and reliability enable high-throughput microbiome analysis in minutes.	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	To update	http://lotus2.earlham.ac.uk/	Metagenomics	lotus2	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2	2.32	lotus2	2.34.1	Sequence feature detection, DNA barcoding	Metagenomics, Taxonomy, Microbial ecology	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	1	0	0	114	936	False
m6anet	m6anet	m6anet to detect m6A RNA modifications from nanopore data	m6Anet	m6Anet	m6Anet	Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework.	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	Up-to-date	https://m6anet.readthedocs.io/en/latest	Sequence Analysis	m6anet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/m6anet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet	2.1.0	m6anet	2.1.0	Quantification, Imputation, Gene expression profiling	RNA-Seq, Transcriptomics, RNA, Machine learning	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	3	False
maaslin2	maaslin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.	maaslin2	maaslin2	MaAsLin2	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.	Filtering, Statistical calculation, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	Up-to-date	http://huttenhower.sph.harvard.edu/maaslin	Metagenomics	maaslin2	iuc	https://github.com/biobakery/Maaslin2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2	1.18.0	bioconductor-maaslin2	1.18.0	Filtering, Standardisation and normalisation, Visualisation	Metagenomics, Statistics and probability	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	29	188	False
mafft	rbc_mafft_add, rbc_mafft	Multiple alignment program for amino acid or nucleotide sequences	MAFFT	MAFFT	MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.	Multiple sequence alignment	Sequence analysis	To update	https://mafft.cbrc.jp/alignment/software/	RNA	mafft	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	https://github.com/bgruening/galaxytools/tree/master/tools/mafft	7.526	mafft	7.525	Multiple sequence alignment	Sequence analysis	2	2	2	2	2	2	2	2	1	0	2	2	0	2	0	2	2	0	817	143045	False
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	0.0.3	biopython	1.70			0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
maker	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	Genome annotation	Genomics, DNA, Sequence analysis	2	2	2	2	2	2	2	2	0	0	1	0	0	0	0	2	2	0	554	5591	False
mapseq	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		k-mer counting	Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	1	0	0	2	167	False
mash	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	Sequence distance matrix generation	Metagenomics, Statistics and probability, Sequence analysis, DNA mutation	2	2	2	2	2	2	2	2	0	0	2	0	0	0	0	2	2	0	27	9763	False
maxbin2	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	Sequence assembly	Metagenomics, Sequence assembly, Microbiology	1	1	1	1	1	1	1	1	0	0	1	0	0	0	1	1	1	0	118	2059	False
maxquant	maxquant, maxquant_mqpar	wrapper for MaxQuant	maxquant	maxquant	MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.	Imputation, Visualisation, Protein quantification, Statistical calculation, Standardisation and normalisation, Heat map generation, Clustering, Principal component plotting	Proteomics experiment, Proteomics, Statistics and probability	Up-to-date	https://www.maxquant.org/	Proteomics	maxquant	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant	2.0.3.0	maxquant	2.0.3.0	Imputation, Visualisation, Protein quantification, Standardisation and normalisation, Heat map generation, Clustering	Proteomics experiment, Proteomics, Statistics and probability	2	2	2	0	2	2	2	0	0	2	0	0	0	0	0	2	2	0	415	6078	False
mcl	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	Clustering, Gene regulatory network analysis	Molecular interactions, pathways and networks	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	10	29	False
medaka	medaka_consensus, medaka_consensus_pipeline, medaka_snp, medaka_variant	Sequence correction provided by ONT Research	medaka	medaka	Medaka	medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly.	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	To update	https://github.com/nanoporetech/medaka	Sequence Analysis		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka	1.7.2	medaka	2.0.0	Base-calling, Variant calling, Sequence assembly	Sequence assembly, Machine learning	3	3	3	3	3	3	3	3	0	0	3	0	0	2	0	3	3	0	768	99863	False
megahit	megahit	An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.	megahit	megahit	MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	Up-to-date	https://github.com/voutcn/megahit	Sequence Analysis, Assembly, Metagenomics	megahit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit	1.2.9	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	0	548	9530	False
megahit_contig2fastg	megahit_contig2fastg	A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg)	megahit	megahit	MEGAHIT	Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible.	Genome assembly	Metagenomics, Sequencing, Ecology, Sequence assembly	To update	https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp	Sequence Analysis, Assembly, Metagenomics	megahit_contig2fastg	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit_contig2fastg	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg	1.1.3	megahit	1.2.9	Genome assembly	Metagenomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	1	0	0	1	0	1	1	0	54	475	False
megan	megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma	MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing).	megan	megan	MEGAN	Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results.	Sequence analysis, Taxonomic classification	Sequence analysis	To update	https://github.com/husonlab/megan-ce	Sequence Analysis	megan	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/megan	https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan	6.21.7	megan	6.25.9	Sequence analysis, Taxonomic classification	Sequence analysis	0	0	7	0	0	0	7	0	0	0	0	0	0	0	0	7	0	0	261	3610	False
meningotype	meningotype	Assign sequence type to N. meningitidis genome assemblies	meningotype	meningotype	meningotype	In silico typing of Neisseria meningitidis contigs.	Genotyping, Multilocus sequence typing	Microbiology, Genotype and phenotype	Up-to-date	https://github.com/MDU-PHL/meningotype	Sequence Analysis	meningotype	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meningotype	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype	0.8.5	meningotype	0.8.5	Multilocus sequence typing	Microbiology, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
merqury	merqury, merquryplot	Merqury is a tool for evaluating genomes assemblies based of k-mer operations.	merqury	merqury	Merqury	Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose.	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	Up-to-date	https://github.com/marbl/merqury	Assembly	merqury	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/merqury	https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury	1.3	merqury	1.3	Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly	Sequence assembly, Whole genome sequencing, Plant biology	2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	1	0	0	244	2483	False
meryl	meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode	Meryl a k-mer counter.	meryl	meryl	Meryl	Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu.	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis, Sequencing	Up-to-date	https://github.com/marbl/meryl	Assembly	meryl	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl	https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl	1.3	merqury	1.3	k-mer counting	Whole genome sequencing, Genomics, Sequence analysis	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
metabat2	metabat2_jgi_summarize_bam_contig_depths, metabat2	MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency.	MetaBAT_2	MetaBAT_2	MetaBAT 2	an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies \| MetaBAT2 clusters metagenomic contigs into different "bins", each of which should correspond to a putative genome \| MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	To update	https://bitbucket.org/berkeleylab/metabat/src/master/	Metagenomics	metabat2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2	2.15	metabat2	2.17	Read binning, Sequence assembly, Genome annotation	Metagenomics, Sequence assembly, Metagenomic sequencing	2	1	2	2	2	1	2	2	0	0	1	0	0	0	1	2	0	0	192	4329	False
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	Homology-based gene prediction	Metagenomics, Gene and protein families	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	16	184	False
metagene_annotator	metagene_annotator	MetaGeneAnnotator gene-finding program for prokaryote and phage	metageneannotator	metageneannotator	MetaGeneAnnotator	Prokaryotic gene finding program from environmental genome shotgun sequences or metagenomic sequences.	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	Up-to-date	http://metagene.nig.ac.jp/	Sequence Analysis	metagene_annotator	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metagene_annotator	1.0	metagene_annotator	1.0	Sequence annotation	Genomics, Model organisms, Data submission, annotation and curation	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	1	1	0	115	636	False
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	https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html	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	Sequence visualisation, Statistical calculation	Metagenomics, Sequencing	1	0	1	1	1	0	1	1	0	0	1	0	0	0	0	1	1	0	6	753	False
metanovo	metanovo	Produce targeted databases for mass spectrometry analysis.	metanovo	metanovo	MetaNovo	An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	Up-to-date	https://github.com/uct-cbio/proteomics-pipelines	Proteomics	metanovo	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metanovo	1.9.4	metanovo	1.9.4	Target-Decoy, de Novo sequencing, Tag-based peptide identification, Protein identification, Expression analysis	Proteomics, Microbial ecology, Metagenomics, Proteomics experiment, Small molecules	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	1	0	0	15	4181	False
metaphlan	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	Up-to-date	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	4.1.1	metaphlan	4.1.1	Nucleic acid sequence analysis	Metagenomics, Phylogenomics	1	2	4	4	1	2	4	4	2	0	4	0	0	0	0	4	4	0	499	11069	False
metaquantome	metaquantome_db, metaquantome_expand, metaquantome_filter, metaquantome_sample, metaquantome_stat, metaquantome_viz	quantitative analysis of microbiome taxonomy and function	metaQuantome	metaQuantome	metaQuantome	metaQuantome software suite analyzes the state of a microbiome by leveraging complex taxonomic and functional hierarchies to summarize peptide-level quantitative information. metaQuantome offers differential abundance analysis, principal components analysis, and clustered heat map visualizations, as well as exploratory analysis for a single sample or experimental condition.	Principal component visualisation, Visualisation, Functional clustering, Query and retrieval, Differential protein expression analysis, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	Up-to-date	https://github.com/galaxyproteomics/metaquantome/	Proteomics	metaquantome	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/metaquantome	2.0.2	metaquantome	2.0.2	Principal component visualisation, Functional clustering, Query and retrieval, Heat map generation, Quantification, Indexing, Filtering, Statistical inference	Proteomics, Metatranscriptomics, Microbial ecology, Proteomics experiment, Metagenomics	0	6	6	0	0	6	6	0	0	0	0	0	0	0	0	6	6	0	104	2522	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	Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing	Whole genome sequencing, Metagenomic sequencing, Metagenomics	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	False
minia	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	Genome assembly	Sequence assembly	0	1	1	0	0	1	1	0	0	0	1	0	0	0	0	1	1	0	109	2206	False
miniasm	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	De-novo assembly	Genomics, Sequence assembly	1	1	1	1	1	1	1	1	0	0	1	0	0	0	0	1	1	0	178	11938	False
minipolish	minipolish	Polishing miniasm assemblies	minipolish	minipolish	minipolish	A tool that bridges the output of miniasm (long-read assembly) and racon (assembly polishing) together to polish a draft assembly. It also provides read depth information in contigs.	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	Up-to-date	https://github.com/rrwick/Minipolish	Sequence Analysis	minipolish	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	https://github.com/bgruening/galaxytools/tree/master/tools/minipolish	0.1.3	minipolish	0.1.3	Localised reassembly, Read depth analysis	Sequence assembly, Sequencing	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	1	0	0	21	185	False
miniprot	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	Sequence alignment, Protein sequence analysis	Sequence sites, features and motifs, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	2	0	0	30	842	False
mitos	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	Genome annotation	Zoology, Whole genome sequencing	1	1	2	0	1	1	2	0	0	0	1	0	0	0	0	2	1	0	236	100920	False
mlst	mlst, mlst_list	Scan contig files against PubMLST typing schemes	mlst	mlst	MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.	Multilocus sequence typing	Immunoproteins and antigens	To update	https://github.com/tseemann/mlst	Sequence Analysis	mlst	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mlst	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst	2.22.0	mlst	2.23.0	Multilocus sequence typing	Immunoproteins and antigens	2	2	2	2	2	2	2	2	0	0	2	0	0	0	0	2	2	0	635	9304	False
mob_suite	mob_recon, mob_typer	MOB-suite is a set of software tools for clustering, reconstruction and typing of plasmids from draft assemblies							To update	https://github.com/phac-nml/mob-suite	Sequence Analysis	mob_suite	nml	https://github.com/phac-nml/mob-suite	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mob_suite	3.0.3	mob_suite	3.1.9			0	2	2	2	0	2	2	2	0	0	2	0	0	0	0	2	0	0	322	89021	False
mothur	mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn	Mothur wrappers	mothur	mothur	mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	To update	https://www.mothur.org	Metagenomics	mothur	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur	1.0	mothur	1.48.0	DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis	Microbial ecology, Taxonomy, Sequence analysis, Phylogeny	129	129	129	129	129	129	129	129	128	0	3	0	0	0	0	129	129	0	14353	302916	False
mrbayes	mrbayes	A program for the Bayesian estimation of phylogeny.							To update		Sequence Analysis	mrbayes	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/mrbayes	1.0.2	mrbayes	3.2.7			0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	False
msconvert	msconvert	msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container	msconvert	msconvert	msConvert	msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.	Filtering, Formatting	Proteomics, Proteomics experiment	To update	http://proteowizard.sourceforge.net/tools.shtml	Proteomics	msconvert	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert	3.0.20287			Filtering, Formatting	Proteomics, Proteomics experiment	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	1	1	0	189	19958	False
msstatstmt	msstatstmt	MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling							To update	http://msstats.org/msstatstmt/	Proteomics	msstatstmt	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msstatstmt	2.0.0	bioconductor-msstatstmt	2.10.0			0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	1	0	0	71	726	False
multigsea	multigsea	GSEA-based pathway enrichment analysis for multi-omics data	multiGSEA	multiGSEA	multiGSEA	A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration.	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	Up-to-date	https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html	Transcriptomics, Proteomics, Statistics	multigsea	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multigsea	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea	1.12.0	bioconductor-multigsea	1.12.0	Gene-set enrichment analysis, Aggregation, Pathway analysis	Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	2	53	False
multiqc	multiqc	MultiQC aggregates results from bioinformatics analyses across many samples into a single report	multiqc	multiqc	MultiQC	MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.	Validation, Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	To update	http://multiqc.info/	Fastq Manipulation, Statistics, Visualization	multiqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc	1.24.1	multiqc	1.25	Sequencing quality control	Sequencing, Bioinformatics, Sequence analysis, Genomics	1	1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	1	0	8320	162790	False
mykrobe	mykrobe_predict	Antibiotic resistance predictions	Mykrobe	Mykrobe	Mykrobe	Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	To update	https://github.com/Mykrobe-tools/mykrobe	Sequence Analysis	mykrobe	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/mykrobe	https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe	0.10.0	mykrobe	0.13.0	Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming	Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
mykrobe_parser	mykrobe_parseR	RScript to parse the results of mykrobe predictor.							To update	https://github.com/phac-nml/mykrobe-parser	Sequence Analysis	mykrobe_parser	nml	https://github.com/phac-nml/mykrobe-parser	https://github.com/phac-nml/galaxy_tools/tree/master/tools/mykrobe_parser	0.1.4.1	r-base				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
mz_to_sqlite	mz_to_sqlite	Creates a SQLite database for proteomics data	mztosqlite	mztosqlite	mzToSQLite	Convert proteomics data files into a SQLite database	Conversion, Peptide database search	Proteomics, Biological databases	To update	https://github.com/galaxyproteomics/mzToSQLite	Proteomics	mz_to_sqlite	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mz_to_sqlite	2.1.1+galaxy0	mztosqlite	2.1.1	Conversion, Peptide database search	Proteomics, Biological databases	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	1	0	33	844	False
nanocompore	nanocompore_db, nanocompore_sampcomp	Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro.	Nanocompore	Nanocompore	Nanocompore	RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro	Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	To update	https://nanocompore.rna.rocks/	Sequence Analysis	nanocompore	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore	1.0.0rc3.post2	nanocompore	1.0.4	PolyA signal detection, Genotyping, k-mer counting	Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites	0	1	2	0	0	1	2	0	0	0	1	0	0	0	0	2	2	0	3	836	False
nanoplot	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	1.43.0	nanoplot	1.43.0	Scatter plot plotting, Box-Whisker plot plotting	Genomics	1	1	1	1	1	1	1	1	1	1	1	0	0	1	0	1	1	0	2195	63235	False
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	Methylation analysis, Collapsing methods	Sequence analysis, Sequencing, Genetic variation	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	2	2	0	15	1074	False
ncbi_blast_plus	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	16	16	16	16	16	16	16	16	15	16	0	0	16	16	16	15	0	4066	365597	False
ncbi_fcs_gx	ncbi_fcs_gx	FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).	ncbi_fcs	ncbi_fcs	NCBI fcs	The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	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	0.5.4	ncbi-fcs-gx	0.5.4	Sequence assembly validation, Sequence trimming, Sequence contamination filtering	Sequence analysis, Sequence assembly	1	0	1	0	1	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	False
newick_utils	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		Phylogeny, Genomics, Computer science	1	1	1	1	1	1	1	1	0	0	1	0	0	0	0	1	1	0	448	25505	False
nextclade	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	Methylation analysis, Variant calling	Genomics, Cladistics	1	1	2	2	1	1	2	2	0	0	2	1	0	1	0	2	0	0	210	4080	False
nextdenovo	nextdenovo	String graph-based de novo assembler for long reads	nextdenovo	nextdenovo	NextDenovo	NextDenovo is a string graph-based de novo assembler for long reads (CLR, HiFi and ONT). It uses a "correct-then-assemble" strategy similar to canu (no correction step for PacBio Hifi reads), but requires significantly less computing resources and storages.	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	To update	https://github.com/Nextomics/NextDenovo	Assembly	nextdenovo	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	https://github.com/bgruening/galaxytools/tree/master/tools/nextdenovo	2.5.0	nextdenovo	2.5.2	De-novo assembly, Genome assembly	Sequencing, Sequence assembly	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	84	268	False
nonpareil	nonpareil	Estimate average coverage in metagenomic datasets	nonpareil	nonpareil	nonpareil	Estimate metagenomic coverage and sequence diversity	Operation		To update	http://nonpareil.readthedocs.io	Metagenomics	nonpareil	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/nonpareil	https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil	3.1.1	nonpareil	3.5.5	Operation		1	0	1	1	1	0	1	1	0	0	1	0	0	0	0	1	1	0	5	142	False
nucleosome_prediction	Nucleosome	Prediction of Nucleosomes Positions on the Genome	nucleosome_prediction	nucleosome_prediction	nucleosome_prediction	Prediction of Nucleosomes Positions on the Genome	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	Up-to-date	https://genie.weizmann.ac.il/software/nucleo_exe.html	Sequence Analysis	nucleosome_prediction	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	https://github.com/bgruening/galaxytools/tree/master/tools/nucleosome_prediction	3.0	nucleosome_prediction	3.0	Prediction and recognition, Nucleosome position prediction, Sequence analysis	Structural genomics, Nucleic acid sites, features and motifs	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	2	861	False
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	Duplication detection	Sequencing	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
obisindicators	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	0	2	1	1	0	2	1	0	0	0	0	0	0	0	1	0	0	4	45	False
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	Sequence analysis, Sequence analysis	Sequence analysis, DNA, Sequencing	0	10	10	10	0	10	10	10	0	0	0	0	0	0	0	10	10	0	503	26251	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			Sequence assembly validation, Differential protein expression profiling	Proteomics, Sequence analysis, Statistics and probability	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	False
orfipy	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	Coding region prediction, Database search, Transcriptome assembly, De-novo assembly	Computer science, RNA-Seq, Transcriptomics, Small molecules	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	0	53	774	False
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	Genome comparison, Genome alignment	Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics	0	1	1	1	0	1	1	1	0	0	0	0	0	0	0	1	0	0	239	1333	False
peptideshaker	fasta_cli, ident_params, peptide_shaker, search_gui	PeptideShaker and SearchGUI							To update	http://compomics.github.io	Proteomics	peptideshaker	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker		searchgui	4.3.9			4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	4	2	0	485	17477	False
pfamscan	pfamscan	Search a FASTA sequence against a library of Pfam HMM.	pfamscan	pfamscan	PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.	Protein sequence analysis	Sequence analysis	Up-to-date	http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/	Sequence Analysis	pfamscan	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	https://github.com/bgruening/galaxytools/tree/master/tools/pfamscan	1.6	pfam_scan	1.6	Protein sequence analysis	Sequence analysis	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	1	0	0	19	165	False
pharokka	pharokka	rapid standardised annotation tool for bacteriophage genomes and metagenomes	pharokka	pharokka	Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.	Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	To update	https://github.com/gbouras13/pharokka	Genome annotation	pharokka	iuc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka	1.3.2	\n pharokka\n		Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly	Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA	0	1	1	0	0	1	1	0	0	0	1	0	0	0	1	1	0	0	74	2565	False
phyloseq	phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_ordination, phyloseq_plot_richness	Handling and analysis of high-throughput microbiome census data	phyloseq	phyloseq	phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	Up-to-date	https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html	Metagenomics	phyloseq	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyloseq	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq	1.46.0	bioconductor-phyloseq	1.46.0	Deposition, Analysis, Visualisation	Microbiology, Sequence analysis, Metagenomics	0	1	4	4	0	1	4	4	4	0	0	0	0	0	0	3	3	0	82	812	False
phyml	phyml	PhyML is a phylogeny software based on the maximum-likelihood principle.	phyml	phyml	PhyML	Phylogenetic estimation software using Maximum Likelihood	Phylogenetic tree generation (maximum likelihood and Bayesian methods)	Phylogenetics, Bioinformatics, Phylogenetics	Up-to-date	http://www.atgc-montpellier.fr/phyml/	Phylogenetics	phyml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml	3.3.20220408	phyml	3.3.20220408		Phylogenetics, Bioinformatics, Phylogenetics	0	1	1	1	0	1	1	1	0	1	1	0	0	0	0	1	1	0	104	1770	False
picrust	picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes	PICRUSt wrappers	picrust	picrust	PICRUSt	PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	To update	https://picrust.github.io/picrust/	Metagenomics	picrust	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust	1.1.1	picrust	1.1.4	Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding	Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing	0	6	5	6	0	6	5	6	0	0	6	0	0	0	0	5	5	0	45	1095	False
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	Up-to-date	https://github.com/picrust/picrust2/wiki	Metagenomics	picrust2	iuc	https://github.com/picrust/picrust2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2	2.5.3	picrust2	2.5.3	Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis	Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing	0	7	7	0	0	7	7	0	0	0	0	0	0	0	0	7	0	0	88	1000	False
plasflow	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	Sequence analysis	Metagenomics	1	1	1	0	1	1	1	0	1	0	0	0	0	0	0	1	1	0	278	22589	False
plasmidfinder	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	Genome assembly, Scaffolding, Multilocus sequence typing	Whole genome sequencing, Sequence assembly, Mapping, Probes and primers	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	0	0	8	22	False
plasmidspades	plasmidspades	Genome assembler for assemblying plasmid							To update		Assembly	plasmidspades	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/plasmidspades	1.1	spades	4.0.0			0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	False
polypolish	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	Genome assembly, Read mapping, Mapping assembly, Sequencing error detection	Sequence assembly, Sequence composition, complexity and repeats, Mapping	0	1	1	1	0	1	1	1	0	0	1	0	0	0	0	1	0	0	24	239	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	Genome annotation	Genomics, Sequence analysis	0	1	1	1	0	1	1	1	0	0	1	0	0	0	0	0	0	0	0	0	False
prokka	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	Coding region prediction, Genome annotation	Genomics, Model organisms, Virology	1	1	1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	0	3233	371445	False
promer	promer4_substitutions	Aligns two sets of contigs and reports amino acid substitutions between them							To update	https://github.com/phac-nml/promer	Assembly	promer	nml	https://github.com/phac-nml/promer	https://github.com/phac-nml/galaxy_tools/tree/master/tools/promer	1.2	python				0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
proteinortho	proteinortho, proteinortho_grab_proteins, proteinortho_summary	Proteinortho is a tool to detect orthologous proteins/genes within different species.	proteinortho	proteinortho	Proteinortho	Proteinortho is a tool to detect orthologous genes within different species	Sequence clustering, Sequence analysis	Comparative genomics	To update	https://gitlab.com/paulklemm_PHD/proteinortho	Proteomics	proteinortho	iuc	https://gitlab.com/paulklemm_PHD/proteinortho	https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho	6.3.1	proteinortho	6.3.2	Sequence clustering, Sequence analysis	Comparative genomics	0	0	3	0	0	0	3	0	0	0	1	0	0	0	0	3	3	0	200	3320	False
pycoqc	pycoqc	QC metrics for ONT Basecalling	pycoqc	pycoqc	pycoQC	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	Up-to-date	https://github.com/tleonardi/pycoQC	Nanopore	pycoqc	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pycoqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc	2.5.2	pycoqc	2.5.2	Sequencing quality control, Statistical calculation	Sequence analysis, Data quality management, Sequencing	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	0	0	350	21123	False
pygenometracks	pygenomeTracks	pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks.	pygenometracks	pygenometracks	pyGenomeTracks	reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:.	Visualisation, Formatting	Model organisms, Imaging, Workflows	To update	https://github.com/deeptools/pyGenomeTracks	Visualization	pygenometracks	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/pygenometracks	https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks	3.8	pygenometracks	3.9	Visualisation, Formatting	Model organisms, Imaging, Workflows	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	1	1	0	377	11332	False
qiime_add_on	qiime_collapse_samples, qiime_make_otu_table	QIIME to perform microbial community analysis	qiime_add_on	qiime_core, qiime_add_on	qiime_add_on	QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	2	2	0	0	2	2	0	0	0	0	0	0	0	2	2	0	68	1909	False
qiime_core	qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file	QIIME to perform microbial community analysis	qiime_core	qiime_core	qiime_core	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	To update	http://www.qiime.org	Metagenomics	qiime	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core		qiime	1.9.1	Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control	Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics	0	0	32	32	0	0	32	32	31	0	1	0	0	0	0	31	31	0	1155	28681	False
qualimap	qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq	Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts.	qualimap	qualimap	QualiMap	Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.	Sequencing quality control	Data quality management	Up-to-date	http://qualimap.bioinfo.cipf.es/	Sequence Analysis, Transcriptomics, SAM	qualimap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap	2.3	qualimap	2.3	Sequencing quality control	Data quality management	4	4	4	1	4	4	4	1	0	0	4	1	0	1	0	4	4	0	1328	664470	False
quast	quast	Quast (Quality ASsessment Tool) evaluates genome assemblies.	quast	quast	QUAST	QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.	Visualisation, Sequence assembly validation	Sequence assembly	Up-to-date	http://quast.bioinf.spbau.ru/	Assembly	quast	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast	5.2.0	quast	5.2.0	Visualisation, Sequence assembly validation	Sequence assembly	1	1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	1	0	3567	51567	False
quickmerge	quickmerge	Merge long-read and hybrid assemblies to increase contiguity	quickmerge	quickmerge	quickmerge	Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads.	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	Up-to-date	https://github.com/mahulchak/quickmerge	Assembly	quickmerge	galaxy-australia	https://github.com/galaxyproject/tools-iuc/tree/master/tools/quickmerge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge	0.3	quickmerge	0.3	Genome assembly, Scaffolding, De-novo assembly, Genotyping	Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	False
racon	racon	Consensus module for raw de novo DNA assembly of long uncorrected reads.	Racon	Racon	Racon	Consensus module for raw de novo DNA assembly of long uncorrected readsRacon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods. It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies.	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	Up-to-date	https://github.com/isovic/racon	Sequence Analysis	racon	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/racon	https://github.com/bgruening/galaxytools/tree/master/tools/racon	1.5.0	racon	1.5.0	Genome assembly, Mapping assembly	Whole genome sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	0	1	0	0	0	0	1	1	0	309	21353	False
rasusa	rasusa	Randomly subsample sequencing reads to a specified coverage	rasusa	rasusa	rasusa	Produces an unbiased subsample of your reads			To update	https://github.com/mbhall88/rasusa	Sequence Analysis	rasusa	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa	2.0.0	rasusa	2.1.0			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	False
raxml	raxml	RAxML - A Maximum Likelihood based phylogenetic inference	raxml	raxml	RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.	Sequence analysis, Phylogenetic tree analysis	Phylogenetics, Sequence analysis	To update	http://www.exelixis-lab.org/web/software/raxml/	Phylogenetics	raxml	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml	https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml	8.2.12	raxml	8.2.13	Sequence analysis	Phylogenetics	1	1	1	1	1	1	1	1	0	0	1	0	0	0	0	1	1	0	383	6808	False
read_it_and_keep	read_it_and_keep	Rapid decontamination of SARS-CoV-2 sequencing reads	read_it_and_keep	read_it_and_keep	read_it_and_keep	Read contamination removal	Filtering, Genome alignment	Pathology, Genomics	To update	https://github.com/GenomePathogenAnalysisService/read-it-and-keep	Sequence Analysis	read_it_and_keep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/read-it-and-keep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep	0.2.2	read-it-and-keep	0.3.0	Filtering, Genome alignment	Pathology, Genomics	1	0	1	0	1	0	1	0	0	0	1	0	0	0	0	1	0	0	71	3370	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	Sequence assembly	Sequence assembly, RNA, Metagenomics, Microbiology	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	False
recentrifuge	recentrifuge	"With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics."	Recentrifuge	Recentrifuge	Recentrifuge	Robust comparative analysis and contamination removal for metagenomics.	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	Up-to-date	https://github.com/khyox/recentrifuge	Metagenomics	recentrifuge	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/recentrifuge	https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge	1.14.1	recentrifuge	1.14.1	Taxonomic classification, Expression analysis, Cross-assembly	Metagenomics, Microbial ecology, Metagenomic sequencing	1	1	1	1	1	1	1	1	1	0	1	0	0	0	0	1	0	0	48	331	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	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	16	False
roary	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	Genome assembly	DNA, Genomics, Mapping	1	1	1	1	1	1	1	1	0	0	1	0	0	0	0	1	1	0	656	12225	False
rseqc	rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin	an RNA-seq quality control package	rseqc	rseqc	RSeQC	Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.	Data handling	Sequencing	Up-to-date	https://code.google.com/p/rseqc/	Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization	rseqc	nilesh	https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc	https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc	5.0.3	rseqc	5.0.3	Data handling	Sequencing	22	22	22	22	22	22	22	22	22	0	0	22	0	22	0	22	22	0	3206	133498	False
salmon	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	Sequence composition calculation, RNA-Seq quantification, Gene expression analysis	RNA-Seq, Transcriptomics	2	2	3	1	2	2	3	1	0	2	1	1	0	2	0	3	3	0	969	61937	False
sarscov2formatter	sarscov2formatter	sarscov2formatter custom script							Up-to-date	https://github.com/nickeener/sarscov2formatter	Sequence Analysis	sarscov2formatter	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2formatter	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter	1.0	sarscov2formatter	1.0			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	7	173	False
sarscov2summary	sarscov2summary	sarscov2summary custom script							To update	https://github.com/nickeener/sarscov2summary	Sequence Analysis	sarscov2summary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/sarscov2summary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary	0.1	sarscov2summary	0.5			1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	140	False
scoary	scoary	Scoary calculates the assocations between all genes in the accessory genome and the traits.	scoary	scoary	Scoary	Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait.	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	Up-to-date	https://github.com/AdmiralenOla/Scoary	Metagenomics	scoary	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/scoary	https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary	1.6.16	scoary	1.6.16	Analysis	Genotype and phenotype, Model organisms, GWAS study, Functional genomics	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	1	0	0	61	676	False
semibin	semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train	SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks	semibin	semibin	SemiBin	Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes.	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	To update	https://semibin.readthedocs.io/en/latest/	Metagenomics	semibin	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin	https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin	2.0.2	semibin	2.1.0	Sequence assembly, Read binning	Metagenomics, Machine learning, Microbial ecology, Sequence assembly	0	0	6	1	0	0	6	1	0	0	0	0	0	0	0	6	0	0	39	542	False
seqkit	seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate	A cross-platform and ultrafast toolkit for FASTA/Q file manipulation	seqkit	seqkit	seqkit	FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.	DNA transcription, Sequence trimming, DNA translation, Sequence conversion	Database management, Sequence analysis	Up-to-date	https://bioinf.shenwei.me/seqkit/	Sequence Analysis	seqkit	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit	2.8.2	seqkit	2.8.2	DNA transcription, Sequence trimming, DNA translation	Database management, Sequence analysis	0	2	5	2	0	2	5	2	0	0	5	0	0	0	0	3	0	0	129	1964	False
seqprep	seqprep	Tool for merging paired-end Illumina reads and trimming adapters.	seqprep	seqprep	SeqPrep	Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads.	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	Up-to-date	https://github.com/jstjohn/SeqPrep	Fastq Manipulation, Sequence Analysis	seqprep	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqprep	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep	1.3.2	seqprep	1.3.2	Nucleic acid design	Genomics, Sequence assembly, Sequencing, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	False
seqsero2	seqsero2	Salmonella serotype prediction from genome sequencing data	seqsero2	seqsero2	SeqSero2	rapid and improved Salmonella serotype determination using whole genome sequencing data \| SeqSero-Salmonella Serotyping by Whole Genome Sequencing \| Salmonella Serotyping by Whole Genome Sequencing \| Online version: http://www.denglab.info/SeqSero2 \| Salmonella serotype prediction from genome sequencing data \| Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 \| Salmonella serotype derterminants databases \| Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode)	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	Up-to-date	https://github.com/denglab/SeqSero2	Sequence Analysis	seqsero2	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqsero2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2	1.3.1	seqsero2	1.3.1	Genome indexing, Antimicrobial resistance prediction, Genome alignment	Whole genome sequencing, Sequence assembly, Genomics	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	12	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	Haplotype mapping, Variant calling	Metagenomics, Sequencing, Genetics	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	False
shovill	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	Genome assembly	Genomics, Microbiology, Sequence assembly	1	1	1	1	1	1	1	1	1	0	1	0	0	0	0	1	1	0	1008	41600	False
sistr_cmd	sistr_cmd	SISTR in silico serotyping tool							To update	https://github.com/phac-nml/sistr_cmd	Sequence Analysis	sistr_cmd	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/sistr_cmd	1.1.1	sistr_cmd	1.1.2			0	1	1	0	0	1	1	0	0	0	1	0	0	0	0	1	1	0	133	2489	False
smallgenomeutilities	smgu_frameshift_deletions_checks	Set of utilities for manipulating small viral genome data.	v-pipe	v-pipe	V-pipe	Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	Up-to-date	https://github.com/cbg-ethz/smallgenomeutilities	Sequence Analysis	smallgenomeutilities	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/smallgenomeutilities	https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities	0.4.1	smallgenomeutilities	0.4.1	Read pre-processing, Sequence alignment, Genetic variation analysis	Genomics, Population genetics, Workflows, Virology, Sequencing	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	6	121	False
smalt	smalt	SMALT aligns DNA sequencing reads with a reference genome.							Up-to-date	http://www.sanger.ac.uk/science/tools/smalt-0	Sequence Analysis	smalt	nml	https://sourceforge.net/projects/smalt/	https://github.com/phac-nml/galaxy_tools/tree/master/tools/smalt	0.7.6	smalt	0.7.6			0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	False
snap	snap, snap_training	SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes.	snap	snap	SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.	Gene prediction	DNA, DNA polymorphism, Genetics	Up-to-date	https://github.com/KorfLab/SNAP	Sequence Analysis	snap	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap	2013_11_29	snap	2013_11_29	Gene prediction	DNA polymorphism, Genetics	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	1	0	133	1349	False
snippy	snippy_core, snippy, snippy_clean_full_aln	Contains the snippy tool for characterising microbial snps	snippy	snippy	snippy	Rapid haploid variant calling and core SNP phylogeny generation.	Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	To update	https://github.com/tseemann/snippy	Sequence Analysis	snippy	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/snippy	https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy		snippy	4.6.0	Phylogenetic tree visualisation, Variant calling	Genomics, Model organisms, DNA polymorphism, Phylogenetics	3	3	3	3	3	3	3	3	0	0	3	0	0	0	0	3	2	0	1372	105708	False
sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	sonneityping	sonneityping	sonneityping	Scripts for parsing Mykrobe predict results for Shigella sonnei.	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	Up-to-date	https://github.com/katholt/sonneityping	Sequence Analysis	sonneityping	iuc	https://github.com/katholt/sonneityping	https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping	20210201	sonneityping	20210201	Antimicrobial resistance prediction, Variant calling, Genotyping	Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	1	0	0	1	1	False
sortmerna	bg_sortmerna	SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatransriptomic data produced by next-generation sequencers.	sortmerna	sortmerna	SortMeRNA	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.	Sequence similarity search, Sequence comparison, Sequence alignment analysis	Metatranscriptomics, Metagenomics	To update	http://bioinfo.lifl.fr/RNA/sortmerna/	RNA	sortmerna	rnateam	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna	4.3.6	sortmerna	4.3.7	Sequence similarity search, Sequence alignment analysis	Metatranscriptomics, Metagenomics	1	1	1	1	1	1	1	1	1	0	1	0	0	0	0	1	1	0	376	18183	False
spades	spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades	SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.	spades	spades, biosyntheticspades, rnaviralspades, plasmidspades, rnaspades, metaviralspades, metaspades, coronaspades, metaplasmidspades	SPAdes	St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.	Genome assembly	Sequence assembly	To update	https://github.com/ablab/spades	Assembly, RNA, Metagenomics	spades	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades	3.15.5	spades	4.0.0	Genome assembly	Sequence assembly	9	9	9	9	9	9	9	9	1	3	8	2	0	3	0	9	3	0	3547	72953	False
spotyping	spotyping	SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads	spotyping	spotyping	SpoTyping	Fast and accurate in silico Mycobacterium spoligotyping from sequence reads.	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	Up-to-date	https://github.com/xiaeryu/SpoTyping-v2.0	Sequence Analysis	spotyping	iuc	https://github.com/xiaeryu/SpoTyping-v2.0/tree/master/SpoTyping-v2.0-commandLine	https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping	2.1	spotyping	2.1	Variant pattern analysis	Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	12	1278	False
sr_bowtie	bowtieForSmallRNA	bowtie wrapper tool to align small RNA sequencing reads							To update	http://artbio.fr	RNA, Next Gen Mappers	sr_bowtie	artbio	https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie	https://github.com/ARTbio/tools-artbio/tree/main/tools/sr_bowtie	2.3.0	bowtie	1.3.1			0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	False
srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens							To update		Sequence Analysis	srst2	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/srst2	0.3.7	srst2	0.2.0			0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	1	0	0	22	205	False
srst2	srst2	SRST2 Short Read Sequence Typing for Bacterial Pathogens	srst2	srst2	srst2	Short Read Sequence Typing for Bacterial Pathogens	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	To update	http://katholt.github.io/srst2/	Metagenomics	srst2	iuc	https://github.com/katholt/srst2	https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2	0.2.0	samtools	1.21	Multilocus sequence typing	Whole genome sequencing, Public health and epidemiology	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	1	0	0	22	205	False
staramr	staramr_search	Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases.							Up-to-date	https://github.com/phac-nml/staramr	Sequence Analysis	staramr	nml	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr	0.10.0	staramr	0.10.0			1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	1	1	0	889	12673	False
stringmlst	stringmlst	Rapid and accurate identification of the sequence type (ST)							To update		Sequence Analysis	stringmlst	nml		https://github.com/phac-nml/galaxy_tools/tree/master/tools/stringmlst	1.1.0	stringMLST	0.6.3			0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	False
structure	structure	for using multi-locus genotype data to investigate population structure.	structure	structure	Structure	The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.	Genetic variation analysis	Population genetics	Up-to-date	https://web.stanford.edu/group/pritchardlab/structure.html	Phylogenetics, Variant Analysis	structure	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/structure	https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure	2.3.4	structure	2.3.4	Genetic variation analysis	Population genetics	0	0	1	1	0	0	1	1	0	0	0	0	0	0	0	1	1	0	59	2623	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	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	3	0	0	6	13	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	2024.5.0+q2galaxy.2024.5.0					4	4	4	2	4	4	4	2	0	0	0	0	0	0	0	4	0	0	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	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	4	0	0	5	67	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	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	4	0	0	31	202	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	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	3	0	0	9	73	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	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	6	0	0	26	114	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_alpha_diversity, 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	2024.5.0+q2galaxy.2024.5.0					21	21	22	21	21	21	22	21	0	0	0	0	0	0	0	21	0	0	43	168	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	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	12	0	0	4	4	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	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	3	0	0	2	6	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	2024.5.0+q2galaxy.2024.5.0					10	10	10	10	10	10	10	10	0	0	0	0	0	0	0	10	0	0	48	263	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	2024.5.0+q2galaxy.2024.5.0					17	17	17	17	17	17	17	17	0	0	0	0	0	0	0	17	0	0	59	213	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	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	3	0	0	6	20	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	2024.5.0+q2galaxy.2024.5.0					11	11	11	11	11	11	11	11	0	0	0	0	0	0	0	11	0	0	6	14	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	2024.5.0+q2galaxy.2024.5.0					3	3	3	3	3	3	3	3	0	0	0	0	0	0	0	3	0	0	40	232	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	2024.5.0+q2galaxy.2024.5.0					12	12	12	12	12	12	12	12	0	0	0	0	0	0	0	12	0	0	12	37	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	2024.5.0+q2galaxy.2024.5.0					6	6	6	6	6	6	6	6	0	0	0	0	0	0	0	6	0	0	0	0	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	2024.5.0+q2galaxy.2024.5.0					1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	1	0	0	2	13	False
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	2024.5.0+q2galaxy.2024.5.0					0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	2024.5.0+q2galaxy.2024.5.0					15	15	15	15	15	15	15	15	0	0	0	0	0	0	0	15	0	0	1	1	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	2024.5.0+q2galaxy.2024.5.0					4	4	4	4	4	4	4	4	0	0	0	0	0	0	0	4	0	0	22	172	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	2024.5.0+q2galaxy.2024.5.0					8	8	8	7	8	8	8	7	0	0	0	0	0	0	0	8	0	0	8	16	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	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	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	2024.5.0+dist.he540b0b0					2	2	2	2	2	2	2	2	0	0	0	0	0	0	0	2	0	0	124	7087	False
t2ps	Draw_phylogram	Draw phylogeny	t2ps	t2ps	Draw phylogeny	"Given taxonomy representation (produced by Fetch taxonomic representation tool) this utility produces a graphical representations of phylogenetic tree in PDF format." - Galaxy tool wrapper	Phylogenetic tree visualisation	Phylogenomics	To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2ps	devteam	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2ps	1.0.0	taxonomy	0.10.0	Phylogenetic tree visualisation	Phylogenomics	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	1	1	0	31	457	False
t2t_report	t2t_report	Summarize taxonomy							To update	https://bitbucket.org/natefoo/taxonomy	Metagenomics	t2t_report	devteam	https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2t_report	https://github.com/galaxyproject/tools-devteam/tree/main/tool_collections/taxonomy/t2t_report	1.0.0	taxonomy	0.10.0			0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	1	1	0	26	947	False
t_coffee	t_coffee	T-Coffee							To update	http://www.tcoffee.org/	Sequence Analysis	t_coffee	earlhaminst	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee	13.45.0.4846264	t-coffee	13.46.0.919e8c6b			0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	70	8690	False
taxonomy_krona_chart	taxonomy_krona_chart	Krona pie chart from taxonomic profile	krona	krona	Krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).	Visualisation	Metagenomics	To update	http://sourceforge.net/projects/krona/	Assembly	taxonomy_krona_chart	crs4	https://github.com/galaxyproject/tools-iuc/tree/master/tools/taxonomy_krona_chart	https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart	2.7.1+galaxy0	krona	2.8.1	Visualisation	Metagenomics	1	1	1	1	1	1	1	1	1	1	1	1	0	0	1	1	1	0	1801	27426	False
tb-profiler	tb_profiler_profile	Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers.	tb-profiler	tb-profiler	tb-profiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).	Antimicrobial resistance prediction		To update	https://github.com/jodyphelan/TBProfiler	Sequence Analysis	tbprofiler	iuc	https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler	6.2.1	tb-profiler	6.3.0	Antimicrobial resistance prediction		1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	1	0	198	5161	False
tooldistillator	tooldistillator, tooldistillator_summarize	ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files	tooldistillator	tooldistillator	ToolDistillator	ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports.	Data handling, Parsing	Microbiology, Bioinformatics, Sequence analysis	Up-to-date	https://gitlab.com/ifb-elixirfr/abromics/tooldistillator	Sequence Analysis	tooldistillator	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator	https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator	0.9	tooldistillator	0.9	Parsing	Microbiology, Bioinformatics, Sequence analysis	2	0	2	2	2	0	2	2	0	0	0	0	0	0	0	0	0	0	0	0	False
transit	gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps	TRANSIT	transit	transit	TRANSIT	A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions.	Transposon prediction	DNA, Sequencing, Mobile genetic elements	To update	https://github.com/mad-lab/transit/	Genome annotation		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit	3.0.2	transit	3.2.3	Transposon prediction	DNA, Sequencing, Mobile genetic elements	5	5	5	0	5	5	5	0	0	0	0	0	0	0	0	5	5	0	84	907	False
transtermhp	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	Transcriptional regulatory element prediction	Transcription factors and regulatory sites	1	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	5	229	False
trim_galore	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	Sequence trimming, Primer removal, Read pre-processing	Sequence analysis	1	1	1	1	1	1	1	1	1	0	1	1	0	0	0	1	1	0	2334	238699	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	0	5	5	5	0	0	5	0	0	0	0	5	0	0	147	8942	False
unicycler	unicycler	Unicycler is a hybrid assembly pipeline for bacterial genomes.	unicycler	unicycler	Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	Up-to-date	https://github.com/rrwick/Unicycler	Assembly	unicycler	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler	https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler	0.5.1	unicycler	0.5.1	Genome assembly, Aggregation	Microbiology, Genomics, Sequencing, Sequence assembly	1	1	1	1	1	1	1	1	0	1	1	1	0	1	0	1	1	0	1558	65732	False
unipept	unipept	Unipept retrieves metaproteomics information	unipept	unipept	Unipept	Metaproteomics data analysis with a focus on interactive data visualizations.	Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	To update	https://github.com/galaxyproteomics/tools-galaxyp	Proteomics	unipept	galaxyp	https://unipept.ugent.be/apidocs	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/unipept	4.5.1	python		Prediction and recognition, Visualisation	Proteomics, Proteogenomics, Biodiversity, Workflows	1	1	1	0	1	1	1	0	1	0	1	0	0	0	0	1	1	0	115	5005	False
uniprotxml_downloader	uniprotxml_downloader	Download UniProt proteome in XML or fasta format							To update		Proteomics	uniprotxml_downloader	galaxyp	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader	2.4.0	requests				0	1	1	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	79	1360	False
usher	usher_matutils, usher	UShER toolkit wrappers	usher	usher	usher	The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods.	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics	To update	https://github.com/yatisht/usher	Phylogenetics	usher	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher	https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher	0.2.1	usher	0.6.3	Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences)	Cladistics, Genotype and phenotype, Phylogenomics	0	0	2	0	0	0	2	0	0	0	0	0	0	0	0	2	0	0	5	1060	False
valet	valet	A pipeline for detecting mis-assemblies in metagenomic assemblies.	valet	valet	VALET	VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies.	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	To update	https://github.com/marbl/VALET	Metagenomics	valet	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/valet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet		valet	1.0	Sequence assembly, Sequence assembly visualisation	Metagenomics, Sequence assembly	1	0	1	1	1	0	1	1	0	0	1	0	0	0	0	1	1	0	20	637	False
vapor	vapor	Classify Influenza samples from raw short read sequence data	vapor	vapor	VAPOR	VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain.	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	Up-to-date	https://github.com/connor-lab/vapor	Sequence Analysis	vapor	iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor	1.0.2	vapor	1.0.2	Data retrieval, De-novo assembly, Read mapping	Whole genome sequencing, Mapping, Sequence assembly	1	0	1	0	1	0	1	0	0	0	0	1	0	0	0	1	0	0	94	3164	False
varvamp	varvamp	Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses	varvamp	varvamp	varVAMP	variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.	PCR primer design	Virology, Probes and primers	To update	https://github.com/jonas-fuchs/varVAMP/	Sequence Analysis	varvamp	iuc	https://github.com/jonas-fuchs/varVAMP	https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp	1.2.0	varvamp	1.2.1	PCR primer design	Virology, Probes and primers	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	False
vegan	vegan_diversity, vegan_fisher_alpha, vegan_rarefaction	an R package fo community ecologist	vegan	vegan	vegan	Ordination methods, diversity analysis and other functions for community and vegetation ecologists	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	To update	https://cran.r-project.org/package=vegan	Metagenomics		iuc	https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/	https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan	2.4-3	r-vegan	2.3_4	Standardisation and normalisation, Analysis	Ecology, Phylogenetics, Environmental science	3	0	3	0	3	0	3	0	0	0	3	0	0	0	0	3	3	0	74	2020	False
velvet	velvetg, velveth	de novo genomic assembler specially designed for short read sequencing technologies	velvet	velvet	Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.	Formatting, De-novo assembly	Sequence assembly	To update	https://www.ebi.ac.uk/~zerbino/velvet/	Assembly	velvet	devteam	https://github.com/galaxyproject/tools-iuc/tree/master/tools/velvet	https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet		velvet	1.2.10	Formatting, De-novo assembly	Sequence assembly	2	2	2	2	2	2	2	2	2	2	0	0	0	0	0	2	0	0	2083	25420	False
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	Optimisation and refinement, Sequence assembly	Genomics, Sequence assembly	1	1	1	0	1	1	1	0	1	1	0	0	0	0	0	1	1	0	255	4741	False
virAnnot	virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv	virAnnot wrappers	virannot	virannot	virAnnot	VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project "Plant Health Bioinformatics Network". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy.	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	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	1.1.0+galaxy0	biopython	1.70	Sequence annotation, Sequence clustering, Sequence cluster visualisation	Metagenomics, Virology, Microbial ecology	0	0	3	3	0	0	3	3	0	0	0	0	0	0	0	0	0	0	0	0	False
vsearch	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	DNA mapping, Chimera detection	Metagenomics, Sequence analysis	8	8	8	8	8	8	8	8	0	8	8	0	0	8	0	8	8	0	182	8507	False
wtdbg	wtdbg	WTDBG is a fuzzy Bruijn graph (FBG) approach to long noisy reads assembly.	wtdbg2	wtdbg2	wtdbg2	Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. Wtdbg2 is able to assemble the human and even the 32Gb Axolotl genome at a speed tens of times faster than CANU and FALCON while producing contigs of comparable base accuracy.	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	Up-to-date	https://github.com/ruanjue/wtdbg2	Assembly	wtdbg	bgruening	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	https://github.com/bgruening/galaxytools/tree/master/tools/wtdbg	2.5	wtdbg	2.5	Genome assembly, De-novo assembly	Sequence assembly, Sequencing	0	0	1	1	0	0	1	1	0	0	1	0	0	0	0	1	1	0	116	1660	False