This page lists bioinformatics tools and software that are installed across several of the BioCommons infrastructure partner systems. Tool / software status on other infrastructure partner systems will be added over time. Note: NCI (if89) in the table refers to the Australian BioCommons Leadership Share (ABLeS) Tools and Workflows repository, located in project allocation if89 at the National Computational Infrastructure (NCI).

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Tool metadata									Availability on Australian compute infrastructures
Tool Name	Description	Registry link	Tool identifier (e.g. module name)	Topic(s)	Publications	Containers available? (BioContainers)	License	Resources / documentation	Galaxy Australia	NCI (Gadi)	NCI (if89)	Pawsey (Setonix)	QRIScloud / UQ-RCC (Bunya)
3D-DNA	3D de novo assembly (3D-DNA) is a pipeline for de novo assembly using HiC.		3d-dna	Sequence assembly Mapping DNA	De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds		MIT						201008
ABRicate	Mass screening of contigs for antimicrobial resistance or virulence genes.		abricate	Genomics Microbiology		ABRicate	GPL-2.0		3 tools Tool Name Description ABRicate List 1.0.1 ABRicate List: List all of abricate's available databases. ABRicate 1.0.1 ABRicate: Mass screening of contigs for antimicrobial and virulence genes ABRicate Summary 1.0.1 ABRicate Summary: Combine ABRicate results into a simple matrix of gene presence/absence				1.0.0-gompi-2021a
ABySS	De novo genome sequence assembler using short reads.		abyss	Sequence assembly	2 publications Publications 10.1101/gr.089532.108 10.1101/gr.214346.116	ABySS	GPL-3.0		ABySS 2.3.7+galaxy0	2.2.3
AGAT	Another Gff Analysis Toolkit (AGAT) Suite of tools to handle gene annotations in any GTF/GFF format.		agat	Genomics	10.5281/zenodo.3552717		GPL-3.0		AGAT 1.4.0+galaxy0		1.4.0
amber	The Assisted Model Building with Energy Refinement tool refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.		amber	Molecular modelling Computational biology	2 publications Publications The Amber biomolecular simulation programs An overview of the Amber biomolecular simulation package				Generate MD topologies for small molecules 21.10+galaxy0	19.19.12 20 20-tools21 22
ambertools	Consists of several independently developed packages that work well by themselves, and with Amber (Assisted Model Building with Energy Refinement) itself. The suite can also be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB), with generalized Born solvent models.		ambertools	Molecular modelling Molecular dynamics	The Amber biomolecular simulation programs				MMPBSA/MMGBSA 21.10+galaxy0
anaconda	Software package specially developed for the study of genes’ primary structure. It uses gene sequences downloaded from public databases, as FASTA and GenBank, and it applies a set of statistical and visualization methods in different ways, to reveal information about codon context, codon usage, nucleotide repeats within open reading frames (ORFeome) and others.		anaconda	DNA Gene expression	Statistical, computational and visualization methodologies to unveil gene primary structure features								2022.05
anndata	From https://anndata.readthedocs.io/en/latest/ "Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray."		anndata		10.1101/2021.12.16.473007		BSD-3-Clause		4 tools Tool Name Description Export AnnData and loom files 0.10.3+galaxy0 Export AnnData and loom files: Interconvert AnnData and Loom formats Import Anndata and loom 0.10.3+galaxy0 Import Anndata and loom: from different format Manipulate AnnData 0.10.3+galaxy0 Manipulate AnnData: object Inspect AnnData 0.10.3+galaxy0 Inspect AnnData: object
annotatemyids	This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here.		annotatemyids				MIT		annotateMyIDs 3.18.0+galaxy0
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.		antismash	Molecular interactions, pathways and networks Gene and protein families	5 publications Publications 10.1093/nar/gkr466 10.1093/nar/gkt449 10.1093/nar/gkv437 10.1093/NAR/GKX319 10.1093/NAR/GKAA978	antiSMASH			Antismash 6.1.1+galaxy1
any2fasta	Convert various sequence formats to FASTA		any2fasta	Data quality management Genomics			GPL-3.0						0.4.2-gcccore-10.3.0
Apollo	Apollo is a genome annotation viewer and editor. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment.		apollo	Data submission, annotation and curation Gene transcripts Genomics Mapping Molecular interactions, pathways and networks	Apollo: a sequence annotation editor.
aragorn	ARAGORN detects tRNA, mtRNA info about tmRNA, and tmRNA genes		aragorn	Functional, regulatory and non-coding RNA Genomics	ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences		Not licensed		tRNA and tmRNA 0.6
argtable			argtable								2.13
Arriba	Arriba is a command-line tool to detect gene fusions from RNA-Seq data based on the STAR aligner. In addition to fusions, it can detect exon duplications/inversions and truncations of genes (i.e., breakpoints in introns and intergenic regions). Arriba is the winner of the DREAM SMC-RNA Challenge.		arriba	Gene transcripts RNA splicing DNA structural variation			MIT		3 tools Tool Name Description Arriba 2.4.0+galaxy1 Arriba: detect gene fusions from STAR aligned RNA-Seq data Arriba Get Filters 2.4.0+galaxy1 Arriba Get Filters: to history Arriba Draw Fusions 2.4.0+galaxy1 Arriba Draw Fusions:
Augustus	AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally.		augustus	Gene transcripts Gene and protein families	9 publications Publications Gene prediction with a hidden Markov model and a new intron submodel Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources 10.1186/gb-2006-7-s1-s11 Using native and syntenically mapped cDNA alignments to improve de novo gene finding A novel hybrid gene prediction method employing protein multiple sequence alignments Simultaneous gene finding in multiple genomes Predicting Genes in Single Genomes with AUGUSTUS Whole-genome annotation with BRAKER Multi-genome annotation with AUGUSTUS	Augustus	Artistic-1.0		2 tools Tool Name Description Augustus 3.4.0+galaxy1 Augustus: gene prediction for prokaryotic and eukaryotic genomes Train Augustus 3.4.0+galaxy1 Train Augustus: ab-initio gene predictor		3.4.03.5.0 3.4.03.5.0		3.4.0-foss-2021a3.5.0-foss-2022a (D) 3.4.0-foss-2021a3.5.0-foss-2022a (D)
autodock_vina	AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.		autodock_vina	Drug discovery Molecular modelling Molecular docking	10.1002/jcc.21334				4 tools Tool Name Description Prepare ligand 1.5.7+galaxy0 Prepare ligand: for docking with Autodock Vina Calculate the box parameters using RDKit 2021.03.5+galaxy0 Calculate the box parameters using RDKit: for an AutoDock Vina job from a ligand or pocket input file (confounding box) Prepare receptor 1.5.7+galaxy0 Prepare receptor: Tool to prepare receptor for docking with Autodock Vina VINA Docking 1.2.3+galaxy0 VINA Docking: tool to perform protein-ligand docking with Autodock Vina
Bakta	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids		bakta	Genomics Data submission, annotation and curation Sequence analysis	10.1099/mgen.0.000685		GPL-3.0		Bakta 1.9.2+galaxy0
bamtools	BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files.		bamtools	Sequencing Data management Sequence analysis	Bamtools: A C++ API and toolkit for analyzing and managing BAM files	bamtools	MIT		5 tools Tool Name Description Operate on and transform BAM 2.5.2+galaxy2 Operate on and transform BAM: datasets in various ways Split BAM by reads mapping status 2.5.2+galaxy2 Split BAM by reads mapping status: into a mapped and an unmapped dataset Split BAM by read tag value 2.5.2+galaxy2 Split BAM by read tag value: into a dataset list collection Filter BAM 2.5.2+galaxy2 Filter BAM: datasets on a variety of attributes Split BAM into paired- and single-end 2.5.2+galaxy2 Split BAM into paired- and single-end: reads datasets		2.5.2	2.5.1--hd03093a_10	2.5.2-gcc-10.3.02.5.2-gcc-11.3.0 (D) 2.5.2-gcc-10.3.02.5.2-gcc-11.3.0 (D)
bamutil_diff	Bamutil provides a serie of programs to work on SAM/BAM files.		bamutil_diff	Data management	An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data		GPL-3.0		BamUtil diff 1.0.15+galaxy1
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.		bandage	Genomics Sequence assembly	10.1093/bioinformatics/btv383	bandage	GPL-3.0		2 tools Tool Name Description Bandage Info 2022.09+galaxy2 Bandage Info: determine statistics of de novo assembly graphs Bandage Image 2022.09+galaxy4 Bandage Image: visualize de novo assembly graphs
barrnap	Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).		barrnap	Genomics Model organisms Model organisms		barrnap	GPL-3.0		barrnap 1.2.2
basespace			basespace										1.5.3 matlab
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.		bbmap	Sequencing RNA splicing Whole genome sequencing Phylogenetics Metagenomics RNA-Seq		bbmap	BSD-3-Clause		BBTools: BBduk 39.08+galaxy0	38.93		38.96--h5c4e2a8_0	38.96-gcc-10.3.039.01-gcc-11.3.0 (D) 38.96-gcc-10.3.039.01-gcc-11.3.0 (D)
bcbiogff	A tool for filling the gap created by genomic data processing/analysis by rebasing some analysis results against the parent features which were originally analysed.		bcbiogff		Biopython: Freely available Python tools for computational molecular biology and bioinformatics				3 tools Tool Name Description Rebase GFF3 features 1.2 Rebase GFF3 features: against parent features Table to GFF3 1.2 Table to GFF3: BlastXML to gapped GFF3 1.1 BlastXML to gapped GFF3:
BCFtools	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.		bcftools	Genetic variation DNA polymorphism GWAS study Genotyping experiment	2 publications Publications The Sequence Alignment/Map format and SAMtools Twelve years of SAMtools and BCFtools	BCFtools	MIT		30 tools Tool Name Description bcftools view 1.15.1+galaxy4 bcftools view: VCF/BCF conversion, view, subset and filter VCF/BCF files bcftools roh 1.15.1+galaxy4 bcftools roh: HMM model for detecting runs of homo/autozygosity bcftools List Samples 1.15.1+galaxy4 bcftools List Samples: in VCF/BCF file bcftools gtcheck 1.15.1+galaxy4 bcftools gtcheck: Check sample identity bcftools concat 1.15.1+galaxy4 bcftools concat: Concatenate or combine VCF/BCF files bcftools stats 1.15.1+galaxy4 bcftools stats: Parses VCF or BCF and produces stats which can be plotted using plot-vcfstats bcftools reheader 1.15.1+galaxy4 bcftools reheader: Modify header of VCF/BCF files, change sample names bcftools query 1.15.1+galaxy4 bcftools query: Extracts fields from VCF/BCF file and prints them in user-defined format bcftools tag2tag 1.15.1+galaxy4 bcftools tag2tag: plugin Convert between similar tags, such as GL and GP bcftools setGT 1.15.1+galaxy4 bcftools setGT: plugin Sets genotypes bcftools mendelian 1.15.1+galaxy4 bcftools mendelian: plugin Count Mendelian consistent / inconsistent genotypes bcftools fill-tags 1.15.1+galaxy4 bcftools fill-tags: plugin Set INFO tags AF, AN, AC, AC_Hom, AC_Het, AC_Hemi bcftools dosage 1.15.1+galaxy4 bcftools dosage: plugin genotype dosage bcftools counts 1.15.1+galaxy4 bcftools counts: plugin counts number of samples, SNPs, INDELs, MNPs and total sites bcftools norm 1.15.1+galaxy4 bcftools norm: Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows bcftools mpileup 1.15.1+galaxy4 bcftools mpileup: Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files bcftools merge 1.15.1+galaxy4 bcftools merge: Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file bcftools filter 1.15.1+galaxy4 bcftools filter: Apply fixed-threshold filters bcftools csq 1.15.1+galaxy4 bcftools csq: Haplotype aware consequence predictor bcftools convert from vcf 1.15.1+galaxy4 bcftools convert from vcf: Converts VCF/BCF to IMPUTE2/SHAPEIT formats bcftools cnv 1.15.1+galaxy4 bcftools cnv: Call copy number variation from VCF B-allele frequency (BAF) and Log R Ratio intensity (LRR) values bcftools annotate 1.15.1+galaxy4 bcftools annotate: Annotate and edit VCF/BCF files bcftools call 1.15.1+galaxy5 bcftools call: SNP/indel variant calling from VCF/BCF bcftools consensus 1.15.1+galaxy4 bcftools consensus: Create consensus sequence by applying VCF variants to a reference fasta file bcftools convert to vcf 1.15.1+galaxy4 bcftools convert to vcf: Converts other formats to VCF/BCFk bcftools isec 1.15.1+galaxy4 bcftools isec: Create intersections, unions and complements of VCF files bcftools fill-AN-AC 1.15.1+galaxy4 bcftools fill-AN-AC: plugin Fill INFO fields AN and AC bcftools fixploidy 1.15.1+galaxy4 bcftools fixploidy: plugin Fix ploidy bcftools impute-info 1.15.1+galaxy4 bcftools impute-info: plugin Add imputation information metrics to the INFO field bcftools missing2ref 1.15.1+galaxy4 bcftools missing2ref: plugin Set missing genotypes	1.9 1.12		1.15--haf5b3da_0	1.12-gcc-10.3.01.15.1-gcc-11.3.0 (D) 1.12-gcc-10.3.01.15.1-gcc-11.3.0 (D)
bcl2fastq2			bcl2fastq2										2.20.0-gcc-11.3.0
Beagle	Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.		beagle	Population genetics	4 publications Publications Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering Genotype Imputation with Millions of Reference Samples Fast two-stage phasing of large-scale sequence data A One-Penny Imputed Genome from Next-Generation Reference Panels	Beagle	GPL-3.0						5.4.22jul22.46e-java-11
beagle-lib	BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.		beagle-lib	Phylogenetics Statistics and probability Computer science	BEAGLE: An application programming interface and high-performance computing library for statistical phylogenetics		GPL-3.0			3.1.2			3.1.2-gcc-11.3.04.0.0-gcc-11.3.0 (D) 3.1.2-gcc-11.3.04.0.0-gcc-11.3.0 (D)
BEAST	The Bayesian Evolutionary Analysis Sampling Trees is a cross-platform program for Bayesian analysis of molecular sequences using MCMC (Markov chain Monte Carlo). It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology.		beast	Phylogenetics Sequence analysis	3 publications Publications Bayesian phylogenetics with BEAUti and the BEAST 1.7 10.1093/ve/vey016 BEAST: Bayesian evolutionary analysis by sampling trees	BEAST				1.10.4		1.10.4
BEAST2	Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. It uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. It includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.		beast2	Phylogenetics Phylogenomics	BEAST 2: A Software Platform for Bayesian Evolutionary Analysis							2.6.7
bed_to_protein_map	Convert a BED format file of the proteins from a proteomics search database into a tabular format for the Multiomics Visualization Platform (MVP).		bed_to_protein_map	Literature and language			Not licensed		bed to protein map 0.2.0
BEDTools	BEDTools is an extensive suite of utilities for comparing genomic features in BED format.		bedtools	Genomics	BEDTools: A flexible suite of utilities for comparing genomic features	BEDTools	GPL-2.0		39 tools Tool Name Description bedtools RandomBed 2.31.1+galaxy0 bedtools RandomBed: generate random intervals in a genome bedtools MapBed 2.31.1.3 bedtools MapBed: apply a function to a column for each overlapping interval bedtools Compute both the depth and breadth of coverage 2.31.1+galaxy0 bedtools Compute both the depth and breadth of coverage: of features in file B on the features in file A (bedtools coverage) bedtools ExpandBed 2.31.1 bedtools ExpandBed: replicate lines based on lists of values in columns bedtools FisherBed 2.31.1+galaxy0 bedtools FisherBed: calculate Fisher statistic between two feature files bedtools SlopBed 2.31.1+galaxy0 bedtools SlopBed: adjust the size of intervals bedtools TagBed 2.31.1 bedtools TagBed: tag BAM alignments based on overlaps with interval files bedtools Genome Coverage 2.31.1 bedtools Genome Coverage: compute the coverage over an entire genome bedtools SubtractBed 2.31.1 bedtools SubtractBed: remove intervals based on overlaps bedtools MultiCovBed 2.31.1 bedtools MultiCovBed: counts coverage from multiple BAMs at specific intervals bedtools AnnotateBed 2.31.1 bedtools AnnotateBed: annotate coverage of features from multiple files bedtools GroupByBed 2.31.1 bedtools GroupByBed: group by common cols and summarize other cols bedtools WindowBed 2.31.1 bedtools WindowBed: find overlapping intervals within a window around an interval bedtools JaccardBed 2.31.1 bedtools JaccardBed: calculate the distribution of relative distances between two files bedtools MergeBED 2.31.1 bedtools MergeBED: combine overlapping/nearby intervals into a single interval bedtools NucBed 2.31.1 bedtools NucBed: profile the nucleotide content of intervals in a FASTA file bedtools BED12 to BED6 2.31.1 bedtools BED12 to BED6: converter bedtools SpacingBed 2.31.1 bedtools SpacingBed: reports the distances between features bedtools FlankBed 2.31.1+galaxy0 bedtools FlankBed: create new intervals from the flanks of existing intervals bedtools SortBED 2.31.1+galaxy0 bedtools SortBED: order the intervals bedtools Intersect intervals 2.31.1+galaxy0 bedtools Intersect intervals: find overlapping intervals in various ways bedtools ReldistBed 2.31.1 bedtools ReldistBed: calculate the distribution of relative distances bedtools MakeWindowsBed 2.31.1 bedtools MakeWindowsBed: make interval windows across a genome bedtools LinksBed 2.31.1 bedtools LinksBed: create a HTML page of links to UCSC locations bedtools ClusterBed 2.31.1 bedtools ClusterBed: cluster overlapping/nearby intervals bedtools getfasta 2.31.1+galaxy0 bedtools getfasta: use intervals to extract sequences from a FASTA file bedtools BED to BAM 2.31.1+galaxy0 bedtools BED to BAM: converter bedtools MaskFastaBed 2.31.1 bedtools MaskFastaBed: use intervals to mask sequences from a FASTA file bedtools ComplementBed 2.31.1+galaxy0 bedtools ComplementBed: Extract intervals not represented by an interval file bedtools Merge BedGraph files 2.31.1 bedtools Merge BedGraph files: combines coverage intervals from multiple BEDGRAPH files bedtools BED to IGV 2.31.1 bedtools BED to IGV: create batch script for taking IGV screenshots bedtools ShuffleBed 2.31.1+galaxy0 bedtools ShuffleBed: randomly redistrubute intervals in a genome bedtools BAM to BED 2.31.1+galaxy0 bedtools BAM to BED: converter bedtools BEDPE to BAM 2.31.1+galaxy0 bedtools BEDPE to BAM: converter bedtools OverlapBed 2.31.1 bedtools OverlapBed: computes the amount of overlap from two intervals bedtools ClosestBed 2.31.1 bedtools ClosestBed: find the closest, potentially non-overlapping interval bedtools Multiple Intersect 2.31.1 bedtools Multiple Intersect: identifies common intervals among multiple interval files bedtools Convert from BAM to FastQ 2.27.1 bedtools Convert from BAM to FastQ: Annotate DESeq2/DEXSeq output tables 1.1.0 Annotate DESeq2/DEXSeq output tables: Append annotation from GTF to differential expression tool outputs	2.28.0		2.30.0--h468198e_3	2.30.0-gcc-10.3.02.30.0-gcc-11.3.0 (D) 2.30.0-gcc-10.3.02.30.0-gcc-11.3.0 (D)
bellerophon	The Bellerophon pipeline, improving de novo transcriptomes and removing chimeras. Bellerophon is a pipeline created to remove falsely assembled chimeric transcripts in de novo transcriptome assemblies. The pipeline can be downloaded as a vragrant virtual machine (https://app.vagrantup.com/bellerophon/boxes/bellerophon). This is recommended, as it avoids backwards compatibility problems with TransRate		bellerophon	Transcriptomics Sequence assembly RNA-Seq Workflows	The Bellerophon pipeline, improving de novo transcriptomes and removing chimeras				Filter and merge 1.0+galaxy1
berokka	Trim, circularise, orient and filter long read bacterial genome assemblies		berokka	Computer science			GPL-3.0		Berokka 0.2.3
bftools			bftools						2 tools Tool Name Description Show image info 5.7.1+galaxy1 Show image info: with Bioformats Convert image format 6.7.0+galaxy3 Convert image format: with Bioformats
Bio-DB-HTS			bio-db-hts										3.01-gcc-11.3.0
bio-searchio-hmmer			bio-searchio-hmmer										1.7.3-gcc-10.3.01.7.3-gcc-11.3.0 (D) 1.7.3-gcc-10.3.01.7.3-gcc-11.3.0 (D)
bio3d	Bio3D is an R package containing utilities for the analysis of protein structure, sequence and trajectory data.		bio3d	Structure analysis Gene and protein families Bioinformatics	The Bio3D packages for structural bioinformatics		GPL-3.0		4 tools Tool Name Description PCA 2.3.4 PCA: - principal component analysis using Bio3D PCA visualization 2.3.4 PCA visualization: - generate trajectories of principal components of atomic motion RMSD Analysis 2.3.4 RMSD Analysis: using Bio3D RMSF Analysis 2.3.4 RMSF Analysis: using Bio3D
biobakery_workflows			biobakery_workflows										3.1
biobambam	Tools for early stage NGS alignment file processing including fast sorting and duplicate marking.		biobambam	Sequencing	Biobambam: Tools for read pair collation based algorithms on BAM files		GPL-3.0			2.0.182
biom-format	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.		biom-format	Laboratory information management Sequence analysis	Orchestrating high-throughput genomic analysis with Bioconductor	biom-format	GPL-2.0		2 tools Tool Name Description Convert 2.1.15+galaxy1 Convert: between BIOM table formats Add metadata 2.1.15+galaxy1 Add metadata: to a BIOM table
Bionano Solve			bionano_solve						Bionano Hybrid Scaffold 3.7.0+galaxy3
bioperl	A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming.		bioperl	Genomics Software engineering Data management	An introduction to BioPerl	bioperl							1.7.8-gcccore-10.3.01.7.8-gcccore-11.3.0 (D) 1.7.8-gcccore-10.3.01.7.8-gcccore-11.3.0 (D)
biopython	Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.		biopython	Bioinformatics Data management Software engineering Computational biology	Biopython: Freely available Python tools for computational molecular biology and bioinformatics		MIT		3 tools Tool Name Description Translate BED transcripts 0.1.0 Translate BED transcripts: cDNA in 3frames or CDS Get open reading frames (ORFs) or coding sequences (CDSs) 0.2.3 Get open reading frames (ORFs) or coding sequences (CDSs): e.g. to get peptides from ESTs Kraken taxonomic report 0.0.3+galaxy1 Kraken taxonomic report: view report of classification for multiple samples		1.79		1.79-foss-2021a1.79-foss-2022a (D) 1.79-foss-2021a1.79-foss-2022a (D)
BioTransformer	BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.		biotransformer	Small molecules Endocrinology and metabolism Metabolomics Carbohydrates NMR	BioTransformer 3.0 - a web server for accurately predicting metabolic transformation products		LGPL-3.0		BioTransformer 3.0.20230403+galaxy3
bismark	Bismark is a tool to map bisulfite treated sequencing reads and perform methylation calling in a quick and easy-to-use fashion.		bismark	Epigenomics Genomics Epigenetics	Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications	bismark	GPL-3.0		4 tools Tool Name Description Bismark Deduplicate 0.22.1 Bismark Deduplicate: Deduplicates reads mapped by Bismark Bismark Pretty Report 0.22.1 Bismark Pretty Report: Generates a graphical HTML report page from report outputs of Bismark Bismark Meth. Extractor 0.22.1+galaxy1 Bismark Meth. Extractor: Reports on methylation status of reads mapped by Bismark Bismark Mapper 0.22.1+galaxy4 Bismark Mapper: Bisulfite reads mapper
BLAST	A tool that finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.		blast	Sequence analysis Bioinformatics	4 publications Publications Basic local alignment search tool Benchmarking the next generation of homology inference tools NCBI BLAST: a better web interface. BLAST: a more efficient report with usability improvements.					2.10.1 2.11.0	2.13.02.14.1 2.13.02.14.1	2.12.0--pl5262h3289130_0	2.11.0-linux_x86_642.13.0--hf3cf87c_0 2.11.0-linux_x86_642.13.0--hf3cf87c_0
BLAST+	A tool that finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.		blast+	Sequence analysis Bioinformatics	4 publications Publications Basic local alignment search tool Benchmarking the next generation of homology inference tools NCBI BLAST: a better web interface. BLAST: a more efficient report with usability improvements.				16 tools Tool Name Description NCBI BLAST+ segmasker 2.14.1+galaxy2 NCBI BLAST+ segmasker: low-complexity regions in protein sequences NCBI BLAST+ convert2blastmask 2.14.1+galaxy2 NCBI BLAST+ convert2blastmask: Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb NCBI BLAST+ makeblastdb 2.14.1+galaxy2 NCBI BLAST+ makeblastdb: Make BLAST database NCBI BLAST+ blastn 2.14.1+galaxy2 NCBI BLAST+ blastn: Search nucleotide database with nucleotide query sequence(s) NCBI BLAST+ tblastx 2.14.1+galaxy2 NCBI BLAST+ tblastx: Search translated nucleotide database with translated nucleotide query sequence(s) NCBI BLAST+ tblastn 2.14.1+galaxy2 NCBI BLAST+ tblastn: Search translated nucleotide database with protein query sequence(s) BLAST XML to tabular 2.14.1+galaxy2 BLAST XML to tabular: Convert BLAST XML output to tabular NCBI get species taxids 2.14.1+galaxy2 NCBI get species taxids: NCBI BLAST+ rpstblastn 2.14.1+galaxy2 NCBI BLAST+ rpstblastn: Search protein domain database (PSSMs) with translated nucleotide query sequence(s) NCBI BLAST+ blastdbcmd entry(s) 2.14.1+galaxy2 NCBI BLAST+ blastdbcmd entry(s): Extract sequence(s) from BLAST database NCBI BLAST+ blastx 2.14.1+galaxy2 NCBI BLAST+ blastx: Search protein database with translated nucleotide query sequence(s) NCBI BLAST+ dustmasker 2.14.1+galaxy2 NCBI BLAST+ dustmasker: masks low complexity regions NCBI BLAST+ makeprofiledb 2.14.1+galaxy2 NCBI BLAST+ makeprofiledb: Make profile database NCBI BLAST+ blastp 2.14.1+galaxy2 NCBI BLAST+ blastp: Search protein database with protein query sequence(s) NCBI BLAST+ rpsblast 2.14.1+galaxy2 NCBI BLAST+ rpsblast: Search protein domain database (PSSMs) with protein query sequence(s) NCBI BLAST+ database info 2.14.1+galaxy2 NCBI BLAST+ database info: Show BLAST database information from blastdbcmd				2.11.0-gompi-2021a2.13.0-gompi-2022a (D) 2.11.0-gompi-2021a2.13.0-gompi-2022a (D)
blat	Fast, accurate spliced alignment of DNA sequences.		blat	Sequence analysis	BLAT - The BLAST-like alignment tool						37		3.7-gcc-11.3.0
Blockbuster	detect blocks of overlapping reads using a gaussian-distribution approach		Blockbuster	Genomics	Evidence for human microRNA-offset RNAs in small RNA sequencing data				blockbuster 0.1.2
BlockClust			BlockClust						BlockClust 1.1.1
BOLT-LMM			bolt-lmm										2.4.1-intel-2022a
Boost	Boost is a set of libraries for the C++ programming language that provides support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing.		boost	Pure mathematics Imaging Software engineering			Other			1.71.0 1.72.0 1.77.0 1.79.0 1.80.0			1.76.0-gcc-10.3.01.79.0-gcc-11.3.0 (D) 1.76.0-gcc-10.3.01.79.0-gcc-11.3.0 (D)
Bowtie	Bowtie is an ultrafast, memory-efficient short read aligner.		bowtie	Mapping Genomics Sequencing Sequence assembly	3 publications Publications Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Benchmarking short sequence mapping tools 10.7490/f1000research.1114334.1	Bowtie			2 tools Tool Name Description Bowtie2 2.5.3+galaxy1 Bowtie2: - map reads against reference genome Map with Bowtie for Illumina 1.2.0 Map with Bowtie for Illumina:				1.3.1-gcc-11.3.0
Bowtie2	Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.		bowtie2	Mapping Genomics Mapping	6 publications Publications Fast gapped-read alignment with Bowtie 2 Benchmarking short sequence mapping tools Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics Comparison of mapping algorithms used in high-throughput sequencing: Application to Ion Torrent data Lacking alignments? The next-generation sequencing mapper segemehl revisited 10.7490/f1000research.1114334.1	Bowtie2	GPL-3.0			2.3.5.1		2.4.5--py36hd4290be_0	2.4.4-gcc-10.3.02.4.5-gcc-11.3.0 (D) 2.4.4-gcc-10.3.02.4.5-gcc-11.3.0 (D)
Bracken	Statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.		bracken	Metagenomics Microbial ecology	Bracken: Estimating species abundance in metagenomics data		GPL-3.0		Bracken 3.0+galaxy0
BRAKER	Pipeline for unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS.		braker	RNA-Seq RNA Workflows	BRAKER1: Unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS				BRAKER3 3.0.6+galaxy2				3.0.3
breseq	Runs Breseq software on a set of fastq files.		breseq	Sequencing Sequence analysis DNA mutation	3 publications Publications Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update 10.7490/f1000research.1114334.1				breseq 0.35.5+0
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.		busco	Sequence assembly Genomics Transcriptomics Sequence analysis	4 publications Publications 10.1093/bioinformatics/btv351 10.1002/CPZ1.323 10.1093/molbev/msx319 10.1093/molbev/msab199	BUSCO			Busco 5.5.0+galaxy0		5.2.15.4.0 5.2.15.4.0		5.4.2-foss-2021a5.4.5-foss-2022a (D) 5.4.2-foss-2021a5.4.5-foss-2022a (D)
Buttery-eel	Accelerated nanopore basecalling with SLOW5 data format.		buttery-eel	Computer science Protein expression Workflows Transcription factors and regulatory sites	Accelerated nanopore basecalling with SLOW5 data format		MIT				0.3.1+guppy6.4.20.4.1+guppy6.5.70.4.2+dorado7.2.130.4.2+guppy6.5.7 0.3.1+guppy6.4.20.4.1+guppy6.5.70.4.2+dorado7.2.130.4.2+guppy6.5.7 0.3.1+guppy6.4.20.4.1+guppy6.5.70.4.2+dorado7.2.130.4.2+guppy6.5.7 0.3.1+guppy6.4.20.4.1+guppy6.5.70.4.2+dorado7.2.130.4.2+guppy6.5.7
bwa	Fast, accurate, memory-efficient aligner for short and long sequencing reads		bwa	Mapping	6 publications Publications Fast and accurate short read alignment with Burrows-Wheeler transform Benchmarking short sequence mapping tools Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics Comparison of mapping algorithms used in high-throughput sequencing: Application to Ion Torrent data Lacking alignments? The next-generation sequencing mapper segemehl revisited Fast and accurate long-read alignment with Burrows-Wheeler transform	bwa	MIT		2 tools Tool Name Description Map with BWA-MEM 0.7.18 Map with BWA-MEM: - map medium and long reads (> 100 bp) against reference genome Map with BWA 0.7.18 Map with BWA: - map short reads (< 100 bp) against reference genome	0.7.17		0.7.17--h7132678_9	0.7.17-gcc-10.3.00.7.17-gcccore-11.3.0 (D) 0.7.17-gcc-10.3.00.7.17-gcccore-11.3.0 (D)
BWA-meth			BWA-meth						bwameth 0.2.7+galaxy0
bwa_mem2	Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine.		bwa-mem2	Mapping	Efficient architecture-aware acceleration of BWA-MEM for multicore systems		MIT		BWA-MEM2 2.2.1+galaxy1	2.2.1		2.2.1--hd03093a_2
bwakit			bwakit								0.7.110.7.17 0.7.110.7.17
bx-python	Tools for manipulating biological data, particularly multiple sequence alignments.		bx-python	Sequence analysis			MIT		13 tools Tool Name Description Base Coverage 1.0.0 Base Coverage: of all intervals Cluster 1.0.0 Cluster: the intervals of a dataset Complement 1.0.0 Complement: intervals of a dataset Concatenate 1.0.1 Concatenate: two BED files Coverage 1.0.0 Coverage: of a set of intervals on second set of intervals Fetch closest non-overlapping feature 4.0.1 Fetch closest non-overlapping feature: for every interval Get flanks 1.0.0 Get flanks: returns flanking region/s for every gene Join 1.0.0 Join: the intervals of two datasets side-by-side Merge 1.0.0 Merge: the overlapping intervals of a dataset Subtract 1.0.0 Subtract: the intervals of two datasets Subtract Whole Dataset 0.1 Subtract Whole Dataset: from another dataset Wiggle-to-Interval 1.0.1 Wiggle-to-Interval: converter Aggregate datapoints 1.1.4 Aggregate datapoints: Appends the average, min, max of datapoints per interval
c3s			c3s						Copernicus Climate Data Store 0.1.0
Cactus	Cactus is a reference-free whole-genome multiple alignment program.		cactus	Genomics Sequence analysis Phylogeny Sequence assembly Mapping Phylogenetics	3 publications Publications Progressive Cactus is a multiple-genome aligner for the thousand-genome era Cactus: Algorithms for genome multiple sequence alignment Cactus graphs for genome comparisons				2 tools Tool Name Description Cactus 2.7.1+galaxy0 Cactus: whole-genome multiple sequence alignment Cactus: export 2.7.1+galaxy0 Cactus: export: whole-genome multiple sequence alignment to other formats	2.0.3
CAMERA	Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments.		camera	Metabolomics	CAMERA: An integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets		GPL-2.0		2 tools Tool Name Description CAMERA.annotate 2.2.4 CAMERA.annotate: CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition. CAMERA.combinexsAnnos 2.2.2 CAMERA.combinexsAnnos: Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.
Canu	De-novo assembly tool for long read chemistry like Nanopore data and PacBio data.		canu	Genomics	Canu: Scalable and accurate long-read assembly via adaptive κ-mer weighting and repeat separation	Canu			Canu assembler 2.2+galaxy0	2.0 2.0t 1.9 2.1.1		2.2--ha47f30e_0	2.2-gcccore-10.3.02.2-gcccore-11.3.0 (D) 2.2-gcccore-10.3.02.2-gcccore-11.3.0 (D)
cap3	Web-based contig assembly.		cap3	Sequence assembly Sequencing Sequence analysis Genetic variation	CAP3: A DNA sequence assembly program				cap3 2.0.0
Cardinal	Implements statistical and computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.		cardinal	Proteomics Data visualisation	10.1093/bioinformatics/btv146		Artistic-2.0		9 tools Tool Name Description MSI plot spectra 3.4.3+galaxy0 MSI plot spectra: mass spectrometry imaging mass spectra plots MSI Qualitycontrol 3.4.3+galaxy0 MSI Qualitycontrol: mass spectrometry imaging QC MSI preprocessing 3.4.3+galaxy0 MSI preprocessing: mass spectrometry imaging preprocessing MSI mz images 3.4.3+galaxy0 MSI mz images: mass spectrometry imaging m/z heatmaps MSI data exporter 3.4.3+galaxy0 MSI data exporter: exports imzML and Analyze7.5 to tabular files MSI combine 3.4.3+galaxy0 MSI combine: combine several mass spectrometry imaging datasets into one MSI classification 3.4.3+galaxy0 MSI classification: spatial classification of mass spectrometry imaging data MSI filtering 3.4.3+galaxy0 MSI filtering: tool for filtering mass spectrometry imaging data MSI segmentation 3.4.3+galaxy0 MSI segmentation: mass spectrometry imaging spatial clustering
CAT	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.		cat_bins	Metagenomics Metagenomic sequencing Taxonomy Sequence assembly	Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT		MIT		2 tools Tool Name Description CAT bins 5.2.3+galaxy0 CAT bins: annotate with taxonomic classification CAT summarise 5.2.3+galaxy0 CAT summarise: the number of contigs or bins assigned to each taxonomic name
cd-hit	Cluster a nucleotide dataset into representative sequences.		cd-hit	Sequencing	5 publications Publications 10.1093/bioinformatics/bts565 10.1093/bioinformatics/btl158 10.1093/bioinformatics/17.3.282 10.1093/bioinformatics/18.1.77 10.1093/bioinformatics/btq003	cd-hit			2 tools Tool Name Description CD-HIT-EST 1.3 CD-HIT-EST: Cluster a nucleotide dataset into representative sequences CD-HIT PROTEIN 1.3 CD-HIT PROTEIN: Cluster a protein dataset into representative sequences		4.8.1		4.8.1-gcc-10.3.04.8.1-gcc-11.3.0 (D) 4.8.1-gcc-10.3.04.8.1-gcc-11.3.0 (D)
CEL-Seq 2	celseq2 is a Python framework for generating the UMI count matrix from CEL-Seq2 sequencing data.		celseq2	RNA-Seq Transcriptomics	CEL-Seq2: Sensitive highly-multiplexed single-cell RNA-Seq		BSD-2-Clause						0.5.3
CellProfiler	Tool for quantifying data from biological images, particularly in high-throughput experiments.		CellProfiler	Imaging Microarray experiment Genotype and phenotype	2 publications Publications CellProfiler™: Free, versatile software for automated biological image analysis ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis	CellProfiler	BSD-3-Clause		23 tools Tool Name Description TrackObjects 3.1.9+galaxy1 TrackObjects: with CellProfiler SaveImages 3.1.9+galaxy2 SaveImages: with CellProfiler RelateObjects 3.1.9+galaxy1 RelateObjects: with CellProfiler MeasureObjectSizeShape 3.1.9+galaxy1 MeasureObjectSizeShape: with CellProfiler MeasureGranularity 3.1.9+galaxy1 MeasureGranularity: with CellProfiler EnhanceOrSuppressFeatures 3.1.9+galaxy1 EnhanceOrSuppressFeatures: with CellProfiler DisplayDataOnImage 3.1.9+galaxy1 DisplayDataOnImage: with CellProfiler Run CellProfiler pipeline 3.1.9+galaxy1 Run CellProfiler pipeline: with CellProfiler 3 ColorToGray 3.1.9+galaxy1 ColorToGray: with CellProfiler Starting Modules 3.1.9+galaxy2 Starting Modules: Load images and metadata ConvertObjectsToImage 3.1.9+galaxy1 ConvertObjectsToImage: with CellProfiler ExportToSpreadsheet 3.1.9+galaxy2 ExportToSpreadsheet: with CellProfiler GrayToColor 3.1.9+galaxy1 GrayToColor: with CellProfiler IdentifyPrimaryObjects 3.1.9+galaxy2 IdentifyPrimaryObjects: with CellProfiler ImageMath 3.1.9+galaxy1 ImageMath: with CellProfiler MaskImage 3.1.9+galaxy1 MaskImage: with CellProfiler MeasureImageAreaOccupied 3.1.9+galaxy1 MeasureImageAreaOccupied: with CellProfiler MeasureImageIntensity 3.1.9+galaxy1 MeasureImageIntensity: with CellProfiler MeasureImageQuality 3.1.9+galaxy1 MeasureImageQuality: with CellProfiler MeasureObjectIntensity 3.1.9+galaxy1 MeasureObjectIntensity: with CellProfiler MeasureTexture 3.1.9+galaxy1 MeasureTexture: with CellProfiler OverlayOutlines 3.1.9+galaxy1 OverlayOutlines: with CellProfiler Tile 3.1.9+galaxy0 Tile: with CellProfiler
cellranger			cellranger								6.1.2		7.1.0
cellxgene	cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the Human Cell Atlas.		cellxgene	Transcriptomics Cell biology	10.1101/2021.04.05.438318		MIT		Interactive CellXgene Environment 1.1.1
checkm	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.		checkm	Genomics Phylogenomics Phylogenetics Taxonomy Metagenomics Data quality management	CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes		GPL-3.0						1.1.3-foss-2021a1.2.2-foss-2022a (D) 1.1.3-foss-2021a1.2.2-foss-2022a (D)
checkm-database	CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.		checkm-database	Genomics Phylogenomics Phylogenetics Taxonomy Metagenomics Data quality management	CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes		GPL-3.0						2015_01_16
ChEMBL	Database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.		chembl	Small molecules Chemical biology Cheminformatics	2 publications Publications ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI) The European Bioinformatics Institute in 2016: Data growth and integration				2 tools Tool Name Description Search ChEMBL database 0.10.1+galaxy4 Search ChEMBL database: for compounds which are similar to a SMILES string ChEMBL structure pipeline 1.0.0+galaxy0 ChEMBL structure pipeline: for curation and standardizing of molecular structures
chemfp	Fast cheminformatics fingerprint search, at your fingertips. Chemfp is a set of command-line tools and a Python library for fingerprint generation and high-performance similarity search. There are two ways to try out chemfp. From the download page page you can request an evaluation copy of the most recent version of chemfp, or you can download an earlier version for no cost under the MIT license		chemfp	Cheminformatics Chemistry Transcription factors and regulatory sites Literature and language	2 publications Publications 10.26434/CHEMRXIV.7877846.V2 The chemfp project				4 tools Tool Name Description Molecule to fingerprint 1.6.1+galaxy0 Molecule to fingerprint: conversion to several different fingerprint formats SDF to Fingerprint 1.6.1+0 SDF to Fingerprint: - extract fingerprints from sdf file metadata Taylor-Butina clustering 1.6.1+0 Taylor-Butina clustering: of molecular fingerprints NxN clustering 1.6.1+0 NxN clustering: of molecular fingerprints
chemicaltoolbox	ChemicalToolbox is a publicly available web server for performing cheminformatics analysis. The ChemicalToolbox provides an intuitive, graphical interface for common tools for downloading, filtering, visualizing and simulating small molecules and proteins. The ChemicalToolbox is based on Galaxy, an open-source web-based platform which enables accessible and reproducible data analysis. There is already an active Galaxy cheminformatics community using and developing tools. Based on their work, we provide four example workflows which illustrate the capabilities of the ChemicalToolbox, covering assembly of a compound library, hole filling, protein-ligand docking, and construction of a quantitative structure-activity relationship (QSAR) model.		chemicaltoolbox	Cheminformatics Molecular modelling Compound libraries and screening Workflows Small molecules	The ChemicalToolbox: Reproducible, user-friendly cheminformatics analysis on the Galaxy platform				3 tools Tool Name Description Online data 0.2 Online data: fetching ... PubChem Download 1.0.0 PubChem Download: as canonical SMILES PubChem Assay Downloader 1.0.0 PubChem Assay Downloader: as canonical SMILES
chipseeker	This package implements functions to retrieve the nearest genes around the peak, annotate the genomic region of the peak, statistical methods for estimating the significance of overlap among ChIP peak data sets, and incorporate GEO database to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses.		chipseeker	ChIP-seq Data visualisation Data mining	ChIP seeker: An R/Bioconductor package for ChIP peak annotation, comparison and visualization	chipseeker	Artistic-2.0		ChIPseeker 1.28.3+galaxy0
ChiRA	ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.		chira	RNA Molecular interactions, pathways and networks Functional, regulatory and non-coding RNA			GPL-3.0		5 tools Tool Name Description ChiRA qauntify 1.4.30 ChiRA qauntify: quantify aligned loci to score the alignments ChiRA merge 1.4.30 ChiRA merge: merge aligned positions ChiRA extract 1.4.31 ChiRA extract: extrat the chimeras ChiRA collapse 1.4.31 ChiRA collapse: deduplicate fastq reads ChiRA map 1.4.30 ChiRA map: map reads to trascriptome
chromeister	An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons (dotplot).		chromeister	Comparative genomics Sequence analysis	Ultra-fast genome comparison for large-scale genomic experiments		GPL-3.0		Chromeister 1.5.a+galaxy1
circexplorer			circexplorer						CIRCexplorer 1.1.9.0
circlator			circlator										1.5.5--py_3
circos	Circos is tool for visualizing data in a circular format. It was developed for genomic data but can work for many other kinds of data as well.		circos	Comparative genomics Data visualisation	2 publications Publications Circos: An information aesthetic for comparative genomics 10.7490/f1000research.1114334.1	circos			12 tools Tool Name Description Circos: Interval to Circos Text Labels 0.69.8+galaxy8 Circos: Interval to Circos Text Labels: reformats interval files to prepare for Circos text labels Circos: Alignments to links 0.69.8+galaxy8 Circos: Alignments to links: reformats alignment files to prepare for Circos Circos: Stack bigWigs as Histogram 0.69.8+galaxy8 Circos: Stack bigWigs as Histogram: reformats for use in Circos stacked histogram plots Circos: Table viewer 0.69.8+galaxy8 Circos: Table viewer: easily creates circos plots from tabular data GC Skew 0.69.8+galaxy8 GC Skew: calculates skew over genomic sequences Circos: Interval to Tiles 0.69.8+galaxy8 Circos: Interval to Tiles: reformats interval files to prepare for Circos tile plots Circos: bigWig to Scatter 0.69.8+galaxy8 Circos: bigWig to Scatter: reformats bigWig files to prepare for Circos 2d scatter/line/histogram plots Circos: Resample 1/2D data 0.69.8+galaxy8 Circos: Resample 1/2D data: reduce numbers of points in a dataset before plotting Circos: Link Density Track 0.69.8+galaxy8 Circos: Link Density Track: reduce links to a density plot Circos 0.69.8+galaxy8 Circos: visualizes data in a circular layout Circos: Bundle Links 0.69.8+galaxy8 Circos: Bundle Links: reduce numbers of links in datasets before plotting Circos Builder 0.9-RC2 Circos Builder: creates circos plots from standard bioinformatics datatypes.
clifinder			clifinder						CLIFinder 0.5.1
climate_stripes			climate_stripes						climate stripes 1.0.1
clinker	Automatic generation of gene cluster comparison figures. Gene cluster comparison figure generator. A d3 chart for generating gene cluster comparison figures. clinker is a pipeline for easily generating publication-quality gene cluster comparison figures. Given a set of GenBank files, clinker will automatically extract protein translations, perform global alignments between sequences in each cluster, determine the optimal display order based on cluster similarity, and generate an interactive visualisation (using clustermap.js) that can be extensively tweaked before being exported as an SVG file. clustermap.js is an interactive, reusable d3 chart designed to visualise homology between multiple gene clusters.		clinker	Molecular interactions, pathways and networks Sequence analysis Workflows Imaging	10.1101/2020.11.08.370650		MIT		clinker 0.0.23+galaxy0
clipkit			clipkit						ClipKIT. Alignment trimming software for phylogenetics. 0.1.0
Clustal Omega	Multiple sequence alignment software. The name is occassionally spelled as ClustalOmega, Clustal Ω, ClustalΩ, Clustal O, ClustalO.		clustalo	Sequence analysis	3 publications Publications 10.1038/msb.2011.75 10.1002/pro.3290 10.1002/0471250953.bi0313s48	Clustal Omega	GPL-2.0				1.2.4	1.2.4--h87f3376_5
clustalw	Multiple sequence alignment software. Old deprecated versions. Even older versions were CLUSTAL and CLUSTAL V (ClustalV).		clustalw	Sequence analysis	5 publications Publications CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools Multiple sequence alignment with the Clustal series of programs CLUSTAL V: Improved software for multiple sequence alignment CLUSTAL: a package for performing multiple sequence alignment on a microcomputer	clustalw			ClustalW 2.1+galaxy1		2.1
ColabFold	ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.		colabfold_batch	Protein folds and structural domains Protein folding, stability and design Structure prediction Sequence sites, features and motifs Metagenomics	2 publications Publications ColabFold: making protein folding accessible to all 10.1101/2021.08.15.456425		MIT				1.4.01.5.2 1.4.01.5.2
Compose text parameter value			compose_text_param						Compose text parameter value 0.1.1
cookiecutter			cookiecutter								2.4.0
Count occurrences of each record			Count1						Count 1.0.3
CPAT (Coding-Potential Assessment Tool)	CPAT (Coding-Potential Assessment Tool) is a logistic regression model-based classifier that can accurately and quickly distinguish protein-coding and noncoding RNAs using pure linguistic features calculated from the RNA sequences. CPAT takes as input the nucleotides sequences or genomic coordinates of RNAs and outputs the probabilities p (0 ≤ p ≤ 1), which measure the likelihood of protein coding.		cpat	Functional, regulatory and non-coding RNA Gene transcripts RNA-Seq Transcription factors and regulatory sites	RNA Coding Potential Prediction Using Alignment-Free Logistic Regression Model	CPAT (Coding-Potential Assessment Tool)	GPL-3.0		CPAT 3.0.5+galaxy1
Crisflash	Software to generate CRISPR guide RNAs against genomes annotated with individual variation.		crisflash	Genetic variation	Crisflash: Open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation		GPL-3.0						1.2.0 star-ccm+
CTSM/FATES-EMERALD			ctsm_fates						CTSM/FATES-EMERALD 2.0.1
cuda			cuda							10.1 11.0.3 11.2.2 11.4.1 11.6.1 11.7.0
cudnn	The NVIDIA CUDA® Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. cuDNN provides highly tuned implementations for standard routines such as forward and backward convolution, pooling, normalization, and activation layers.		cudnn	Machine learning						7.6.5-cuda10.1 8.1.1-cuda11 8.2.2-cuda11.4 8.6.0-cuda11
Cufflinks	Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one.		cufflinks	RNA splicing Transcriptomics RNA-Seq	5 publications Publications Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Identification of novel transcripts in annotated genomes using RNA-seq Differential analysis of gene regulation at transcript resolution with RNA-seq Improving RNA-Seq expression estimates by correcting for fragment bias 10.7490/f1000research.1114334.1	Cufflinks	BSL-1.0		5 tools Tool Name Description Cuffcompare 2.2.1.2 Cuffcompare: compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments Cufflinks 2.2.1.3 Cufflinks: transcript assembly and FPKM (RPKM) estimates for RNA-Seq data Cuffmerge 2.2.1.3 Cuffmerge: merge together several Cufflinks assemblies Cuffnorm 2.2.1.3 Cuffnorm: Create normalized expression levels Cuffquant 2.2.1.1 Cuffquant: Precompute gene expression levels
cummeRbund	Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.		cummeRbund	Sequencing	Erratum: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks (Nature Protocols (2012) 7 (562-578))	cummeRbund	Artistic-2.0		cummeRbund 2.16.0+galaxy1
customProDB	Generate customized protein sequence database from RNA-Seq data for proteomics search.		customprodb	Data integration and warehousing RNA-Seq Sequencing	CustomProDB: An R package to generate customized protein databases from RNA-Seq data for proteomics search		Artistic-2.0		CustomProDB 1.22.0
cutadapt	Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.		cutadapt	Genomics Probes and primers Sequencing	2 publications Publications 10.14806/ej.17.1.200 10.7490/f1000research.1114334.1		MIT		Cutadapt 4.9+galaxy1		3.7	3.7--py38hbff2b2d_0	3.4-gcccore-10.3.04.2-gcccore-11.3.0 (D) 3.4-gcccore-10.3.04.2-gcccore-11.3.0 (D)
cuteSV	Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis		cutesv	DNA structural variation Sequencing Computer science	2 publications Publications 10.1101/780700 Long-read-based human genomic structural variation detection with cuteSV		MIT		cuteSV 1.0.8+galaxy0		1.0.13
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.		dada2	Sequencing Genetic variation Microbial ecology Metagenomics	10.1038/nmeth.3869		GPL-3.0		10 tools Tool Name Description dada2: sequence counts 1.30.0+galaxy0 dada2: sequence counts: dada2: removeBimeraDenovo 1.30.0+galaxy0 dada2: removeBimeraDenovo: Remove bimeras from collections of unique sequences dada2: plotQualityProfile 1.30.0+galaxy0 dada2: plotQualityProfile: plot a visual summary of the quality scores dada2: plotComplexity 1.30.0+galaxy0 dada2: plotComplexity: Plot sequence complexity profile dada2: mergePairs 1.30.0+galaxy0 dada2: mergePairs: Merge denoised forward and reverse reads dada2: learnErrors 1.30.0+galaxy0 dada2: learnErrors: Learn Error rates dada2: filterAndTrim 1.30.0+galaxy0 dada2: filterAndTrim: Filter and trim short read data dada2: assignTaxonomy and addSpecies 1.30.0+galaxy0 dada2: assignTaxonomy and addSpecies: Learn Error rates dada2: dada 1.30.0+galaxy0 dada2: dada: Remove sequencing errors dada2: makeSequenceTable 1.30.0+galaxy0 dada2: makeSequenceTable: construct a sequence table (analogous to OTU table)
dadi			dadi										2.0.5
datamash			datamash						Datamash 1.8+galaxy0
dbbuilder			dbbuilder						Protein Database Downloader 0.3.4
dcm2niix			dcm2niix								1.0.202207201.0.20230411 1.0.202207201.0.20230411
DeepConsensus (CPU)			deepconsensus-cpu								1.0.0
DeepConsensus (GPU)			deepconsensus-gpu								1.2.0
DeepTools	User-friendly tools for the normalization and visualization of deep-sequencing data.		deeptools	Genomics ChIP-seq	DeepTools: A flexible platform for exploring deep-sequencing data	DeepTools	GPL-3.0		17 tools Tool Name Description bamCompare 3.5.4+galaxy0 bamCompare: normalizes and compares two BAM or CRAM files to obtain the ratio, log2ratio or difference between them bamCoverage 3.5.4+galaxy0 bamCoverage: generates a coverage bigWig file from a given BAM or CRAM file bamPEFragmentSize 3.5.4+galaxy0 bamPEFragmentSize: Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files bigwigCompare 3.5.4+galaxy0 bigwigCompare: normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference between them computeGCBias 3.5.4+galaxy0 computeGCBias: Determine the GC bias of your sequenced reads computeMatrix 3.5.4+galaxy0 computeMatrix: prepares data for plotting a heatmap or a profile of given regions computeMatrixOperations 3.5.4+galaxy0 computeMatrixOperations: Modify or combine the output of computeMatrix in a variety of ways. correctGCBias 3.5.4+galaxy0 correctGCBias: uses the output from computeGCBias to generate GC-corrected BAM/CRAM files multiBamSummary 3.5.4+galaxy0 multiBamSummary: calculates average read coverages for a list of two or more BAM/CRAM files multiBigwigSummary 3.5.4+galaxy0 multiBigwigSummary: calculates average scores for a list of two or more bigwig files plotCorrelation 3.5.4+galaxy0 plotCorrelation: Create a heatmap or scatterplot of correlation scores between different samples plotCoverage 3.5.4+galaxy0 plotCoverage: assesses the sequencing depth of BAM/CRAM files plotEnrichment 3.5.4+galaxy0 plotEnrichment: plots read/fragment coverage over sets of regions plotFingerprint 3.5.4+galaxy0 plotFingerprint: plots profiles of BAM files; useful for assessing ChIP signal strength plotHeatmap 3.5.4+galaxy0 plotHeatmap: creates a heatmap for score distributions across genomic regions plotPCA 3.5.4+galaxy0 plotPCA: Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output plotProfile 3.5.4+galaxy0 plotProfile: creates a profile plot for score distributions across genomic regions				3.5.0-foss-2021a3.5.2-foss-2022a (D) 3.5.0-foss-2021a3.5.2-foss-2022a (D)
dendropy	DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats.		dendropy	Phylogenetics Phylogenomics	DendroPy: A Python library for phylogenetic computing	dendropy	BSD-3-Clause						4.5.2-gcccore-10.3.04.5.2-gcccore-11.3.0 (D) 4.5.2-gcccore-10.3.04.5.2-gcccore-11.3.0 (D)
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.		deseq2	RNA-Seq	Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2		LGPL-2.1		DESeq2 2.11.40.8+galaxy0
DEXSeq	The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.		DEXSeq	RNA-Seq	Drift and conservation of differential exon usage across tissues in primate species	DEXSeq	GPL-3.0		3 tools Tool Name Description plotDEXSeq 1.48.0+galaxy0 plotDEXSeq: Visualization of the per gene DEXSeq results DEXSeq 1.48.0+galaxy0 DEXSeq: Determines differential exon usage from count tables DEXSeq-Count 1.48.0+galaxy0 DEXSeq-Count: Prepare and count exon abundancies from RNA-seq data
Dfam	The Dfam database is a open collection of Transposable Element DNA sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome annotations.		dfam	DNA Phylogeny Mobile genetic elements Sequence assembly Plant biology	10.21203/RS.3.RS-76062/V1								3.3--hdfd78af_0
DIA-NN	Neural networks and interference correction enable deep proteome coverage in high throughput. DIA-NN - a fast and easy to use tool for processing data independent acquisition (DIA) proteomics data. None required (for .raw, .mzML and .dia processing). Two executables are provided: DiaNN.exe (a command-line tool) and DIA-NN.exe (a GUI implemented as a wrapper for DiaNN.exe)		diann	Proteomics Proteomics experiment Sequence analysis Machine learning Small molecules	DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput				DIA-NN 1.8.1+galaxy3
DIA-Umpire	DIA-Umpire is an open source Java program for computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data. It enables untargeted peptide and protein identification and quantitation using DIA data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation.		diaumpire	Proteomics Proteomics experiment	DIA-Umpire: Comprehensive computational framework for data-independent acquisition proteomics		Apache-2.0		DIA_Umpire_SE 2.1.3.0
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.		diamond	Sequence analysis Proteins	Fast and sensitive protein alignment using DIAMOND		AGPL-3.0		3 tools Tool Name Description Diamond 2.0.15+galaxy0 Diamond: alignment tool for short sequences against a protein database Diamond view 2.0.15+galaxy0 Diamond view: generate formatted output from DAA files Diamond makedb 2.0.15+galaxy0 Diamond makedb: Build database from a FASTA file		2.1.9	2.0.14--hdcc8f71_0	2.0.13-gcc-10.3.02.1.0-gcc-11.3.0 (D)2.1.7 2.0.13-gcc-10.3.02.1.0-gcc-11.3.0 (D)2.1.7 2.0.13-gcc-10.3.02.1.0-gcc-11.3.0 (D)2.1.7
diapysef	diaPASEF is an appproch for parallel accumulation-serial fragmentation combined with data-independent acquisition.		diapysef	Proteomics experiment Proteomics Sequence analysis Sequencing Small molecules	diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition				diapysef library generation 0.3.5.0
diffbind	Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.		diffbind	ChIP-seq	VAV3 mediates resistance to breast cancer endocrine therapy		Artistic-2.0		DiffBind 3.12.0+galaxy0
Dorado	Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.		dorado	Sequence analysis					2 tools Tool Name Description Dorado 0.7.3+6e6c45c+galaxy0 Dorado: basecaller for raw Oxford Nanopore data fast5 to pod5 0.7.3+6e6c45c+galaxy0 fast5 to pod5: converter for raw Oxford Nanopore data
DRAGEN ORA			orad								2.6.1
drishti			drishti							3.0 3.0.1
dropletutils	Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.		dropletutils	Gene expression RNA-seq Sequencing Transcriptomics	2 publications Publications 10.1101/234872 10.1101/177048		GPL-3.0		DropletUtils 1.10.0+galaxy2
dwt			dwt						5 tools Tool Name Description Compute P-values and Correlation Coefficients for Feature Occurrences 1.0.1 Compute P-values and Correlation Coefficients for Feature Occurrences: between two datasets using Discrete Wavelet Transfoms Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features 1.0.1 Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features: between two datasets using Discrete Wavelet Transfoms Compute P-values and Second Moments for Feature Occurrences 1.0.1 Compute P-values and Second Moments for Feature Occurrences: between two datasets using Discrete Wavelet Transfoms Compute P-values and Max Variances for Feature Occurrences 1.0.1 Compute P-values and Max Variances for Feature Occurrences: in one dataset using Discrete Wavelet Transfoms Wavelet variance 1.0.2 Wavelet variance: using Discrete Wavelet Transfoms
EagleImp	Fast and Accurate Genome-wide Phasing and Imputation in a Single Tool.		eagleimp	Genotype and phenotype Sequencing GWAS study DNA Computer science	10.1101/2022.01.11.475810		GPL-3.0						1.10
easybuild	EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.		easybuild	Computer science			GPL-2.0						4.8.0
edger	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.		edger	Genetics RNA-Seq ChIP-seq	3 publications Publications Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation edgeR: A Bioconductor package for differential expression analysis of digital gene expression data From reads to genes to pathways: Differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline	edger	GPL-2.0		edgeR 3.36.0+galaxy4
edger-repenrich	Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.		edger-repenrich	Genetics RNA-Seq ChIP-seq	3 publications Publications Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation edgeR: A Bioconductor package for differential expression analysis of digital gene expression data From reads to genes to pathways: Differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline		GPL-2.0		edgeR-repenrich 1.5.2
edirect	Entrez Direct (EDirect) is a command-line tool for Entrez databases. EDirect connects to Entrez through the Entrez Programming Utilities interface. It supports searching by indexed terms, looking up precomputed neighbors or links, filtering results by date or category, and downloading record summaries or reports.		edirect	Data integration and warehousing			Freeware						16.2
eggNOG-mapper	For fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional information from fine-grained orthologs only. Its common uses include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. The use of orthology predictions for functional annotation permits a higher precision than traditional homology searches, as it avoids transferring annotations from close paralogs.		eggnog-mapper	Metagenomics Genomics	3 publications Publications ProGenomes: A resource for consistent functional and taxonomic annotations of prokaryotic genomes Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale		GPL-3.0		3 tools Tool Name Description eggNOG Mapper 2.1.8+galaxy4 eggNOG Mapper: functional sequence annotation by orthology eggNOG Mapper 2.1.8+galaxy4 eggNOG Mapper: annotation phase eggNOG Mapper 2.1.8+galaxy4 eggNOG Mapper: search phase
egsea	This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing.		egsea	Systems biology	Combining multiple tools outperforms individual methods in gene set enrichment analyses	egsea			EGSEA 1.20.0
elastix	Evaluation of an Open Source Registration Package for Automatic Contour Propagation in Online Adaptive Intensity-Modulated Proton Therapy of Prostate Cancer. Home : About : FAQ : wiki : Download : News : Legal stuff : Documentation. Welcome to elastix : a toolbox for rigid and nonrigid registration of images. elastix is open source software, based on the well-known Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting. Nowadays elastix is accompanied by SimpleElastix , making it available in languages like C++, Python, Java, R, Ruby, C# and Lua.		elastix	Medical imaging Oncology Model organisms	3 publications Publications Elastix: A toolbox for intensity-based medical image registration Fast parallel image registration on CPU and GPU for diagnostic classification of Alzheimer's disease Evaluation of an Open Source Registration Package for Automatic Contour Propagation in Online Adaptive Intensity-Modulated Proton Therapy of Prostate Cancer						4.9.05.1.0 4.9.05.1.0
EMBOSS (European Molecular Biology Open Software Suite)	Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool.		emboss	Molecular biology Sequence analysis Biology	EMBOSS: The European Molecular Biology Open Software Suite	EMBOSS (European Molecular Biology Open Software Suite)			107 tools Tool Name Description dreg 5.0.0+galaxy1 dreg: Regular expression search of a nucleotide sequence octanol 5.0.0.1 octanol: Displays protein hydropathy wordmatch 5.0.0.1 wordmatch: Finds all exact matches of a given size between 2 sequences cpgreport 5.0.0.1 cpgreport: Reports all CpG rich regions sixpack 5.0.0.1 sixpack: Display a DNA sequence with 6-frame translation and ORFs plotorf 5.0.0 plotorf: Plot potential open reading frames diffseq 5.0.0.1 diffseq: Find differences between nearly identical sequences needle 5.0.0.1 needle: Needleman-Wunsch global alignment pepcoil 5.0.0.1 pepcoil: Predicts coiled coil regions pepinfo 5.0.0.1 pepinfo: Plots simple amino acid properties in parallel revseq 5.0.0 revseq: Reverse and complement a sequence sigcleave 5.0.0.1 sigcleave: Reports protein signal cleavage sites newcpgseek 5.0.0.1 newcpgseek: Reports CpG rich region pepwindow 5.0.0.1 pepwindow: Displays protein hydropathy noreturn 5.0.0 noreturn: Removes carriage return from ASCII files textsearch 5.0.0 textsearch: Search sequence documentation. Slow, use SRS and Entrez! cusp 5.0.0 cusp: Create a codon usage table showfeat 5.0.0.1 showfeat: Show features of a sequence tranalign 5.0.0 tranalign: Align nucleic coding regions given the aligned proteins geecee 5.0.0 geecee: Calculates fractional GC content of nucleic acid sequences supermatcher 5.0.0.1 supermatcher: Match large sequences against one or more other sequences codcmp 5.0.0 codcmp: Codon usage table comparison etandem 5.0.0.1 etandem: Looks for tandem repeats in a nucleotide sequence biosed 5.0.0 biosed: Replace or delete sequence sections coderet 5.0.0 coderet: Extract CDS, mRNA and translations from feature tables cai 5.0.0 cai: CAI codon adaptation index est2genome 5.0.0.1 est2genome: Align EST and genomic DNA sequences prettyplot 5.0.0.1 prettyplot: Displays aligned sequences, with colouring and boxing nthseq 5.0.0.1 nthseq: Writes one sequence from a multiple set of sequences lindna 5.0.0.1 lindna: Draws linear maps of DNA constructs degapseq 5.0.0 degapseq: Removes gap characters from sequences primersearch 5.0.0.1 primersearch: Searches DNA sequences for matches with primer pairs tcode 5.0.0.1 tcode: Fickett TESTCODE statistic to identify protein-coding DNA polydot 5.0.0.1 polydot: Displays all-against-all dotplots of a set of sequences dotmatcher 5.0.0.1 dotmatcher: Displays a thresholded dotplot of two sequences fuzznuc 5.0.3 fuzznuc: Nucleic acid pattern search garnier 5.0.0 garnier: Predicts protein secondary structure equicktandem 5.0.0.1 equicktandem: Finds tandem repeats fuzzpro 5.0.0.1 fuzzpro: Protein pattern search vectorstrip 5.0.0.1 vectorstrip: Strips out DNA between a pair of vector sequences merger 5.0.0.1 merger: Merge two overlapping nucleic acid sequences prettyseq 5.0.0.1 prettyseq: Output sequence with translated ranges pepstats 5.0.0 pepstats: Protein statistics plotcon 5.0.0.1 plotcon: Plot quality of conservation of a sequence alignment notseq 5.0.0 notseq: Exclude a set of sequences and write out the remaining ones skipseq 5.0.0.1 skipseq: Reads and writes sequences, skipping first few dotpath 5.0.0.1 dotpath: Non-overlapping wordmatch dotplot of two sequences shuffleseq 5.0.0.1 shuffleseq: Shuffles a set of sequences maintaining composition patmatdb 5.0.0 patmatdb: Search a protein sequence with a motif isochore 5.0.0.1 isochore: Plots isochores in large DNA sequences dottup 5.0.0.1 dottup: Displays a wordmatch dotplot of two sequences pepwindowall 5.0.0.1 pepwindowall: Displays protein hydropathy of a set of sequences matcher 5.0.0.1 matcher: Finds the best local alignments between two sequences pepwheel 5.0.0.1 pepwheel: Shows protein sequences as helices maskseq 5.0.0 maskseq: Mask off regions of a sequence trimseq 5.0.0.1 trimseq: Trim ambiguous bits off the ends of sequences infoseq 5.0.0 infoseq: Displays some simple information about sequences freak 5.0.0.1 freak: Residue/base frequency table or plot hmoment 5.0.0.1 hmoment: Hydrophobic moment calculation sirna 5.0.0 sirna: Finds siRNA duplexes in mRNA backtranseq 6.6.0 backtranseq: Back translate a protein sequence wobble 5.0.0.1 wobble: Wobble base plot chips 5.0.0 chips: Codon usage statistics marscan 5.0.0 marscan: Finds MAR/SAR sites in nucleic sequences transeq 5.0.0 transeq: Translate nucleic acid sequences twofeat 5.0.0.1 twofeat: Finds neighbouring pairs of features in sequences union 5.0.0 union: Reads sequence fragments and builds one sequence chaos 5.0.0 chaos: Create a chaos game representation plot for a sequence pasteseq 5.0.0.1 pasteseq: Insert one sequence into another megamerger 5.0.0.1 megamerger: Merge two large overlapping nucleic acid sequences iep 5.0.0.1 iep: Calculates the isoelectric point of a protein newcpgreport 5.0.0.1 newcpgreport: Report CpG rich areas wordcount 5.0.0.1 wordcount: Counts words of a specified size in a DNA sequence descseq 5.0.0 descseq: Alter the name or description of a sequence extractseq 5.0.0 extractseq: Extract regions from a sequence einverted 5.0.0.1 einverted: Finds DNA inverted repeats fuzztran 5.0.0.1 fuzztran: Protein pattern search after translation cutseq 5.0.0.1 cutseq: Removes a specified section from a sequence dan 5.0.0.1 dan: Calculates DNA RNA/DNA melting temperature banana 5.0.0 banana: Bending and curvature plot in B-DNA compseq 5.0.0.1 compseq: Count composition of dimer/trimer/etc words in a sequence splitter 5.0.0.1 splitter: Split a sequence into (overlapping) smaller sequences tmap 5.0.0 tmap: Displays membrane spanning regions msbar 5.0.0.1 msbar: Mutate sequence beyond all recognition digest 5.0.0 digest: Protein proteolytic enzyme or reagent cleavage digest trimest 5.0.0.1 trimest: Trim poly-A tails off EST sequences oddcomp 5.0.0.1 oddcomp: Find protein sequence regions with a biased composition maskfeat 5.0.0 maskfeat: Mask off features of a sequence seqret 5.0.0 seqret: Reads and writes sequences cirdna 5.0.0 cirdna: Draws circular maps of DNA constructs syco 5.0.0.1 syco: Synonymous codon usage Gribskov statistic plot btwisted 5.0.0 btwisted: Calculates the twisting in a B-DNA sequence extractfeat 5.0.0.1 extractfeat: Extract features from a sequence getorf 5.0.0.1 getorf: Finds and extracts open reading frames (ORFs) newseq 5.0.0 newseq: Type in a short new sequence antigenic 5.0.0.1 antigenic: Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. charge 5.0.0.1 charge: Protein charge plot helixturnhelix 5.0.0.1 helixturnhelix: Report nucleic acid binding motifs checktrans 5.0.0.1 checktrans: Reports STOP codons and ORF statistics of a protein water 5.0.0.1 water: Smith-Waterman local alignment pepnet 5.0.0 pepnet: Displays proteins as a helical net seqmatchall 5.0.0.1 seqmatchall: All-against-all comparison of a set of sequences cai custom 5.0.0 cai custom: CAI codon adaptation index using custom codon usage file epestfind 5.0.0.1 epestfind: Finds PEST motifs as potential proteolytic cleavage sites cpgplot 5.0.0 cpgplot: Plot CpG rich areas palindrome 5.0.0.1 palindrome: Looks for inverted repeats in a nucleotide sequence preg 5.0.0+galaxy1 preg: Regular expression search of a protein sequence
ENA upload	A globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and experimental design. Serving both as the database of record for the output of the world's sequencing activity and as a platform for the management, sharing and publication of sequence data.		ena_upload	Data submission, annotation and curation Transcription factors and regulatory sites Gene transcripts Nucleic acid sites, features and motifs	2 publications Publications European nucleotide archive in 2016 10.1093/BIOINFORMATICS/BTAB421				2 tools Tool Name Description ENA Upload tool 0.7.3+galaxy1 ENA Upload tool: Submission of (meta)data to the European Nucleotide Archive (ENA) ENA upload table builder 0.1.0+galaxy0 ENA upload table builder: create tables for the ENA upload tool from metadata templates
EncyclopeDIA	EncyclopeDIA is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries.		encyclopedia	Proteomics Proteomics experiment	Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry		Apache-2.0		4 tools Tool Name Description Walnut 1.12.34+galaxy0 Walnut: PeCAn-based Peptide Detection Directly from Data-Independent Acquisition (DIA) MS/MS Data SearchToLib 1.12.34+galaxy0 SearchToLib: Build a Chromatogram Library from Data-Independent Acquisition (DIA) MS/MS Data EncyclopeDIA 1.12.34+galaxy0 EncyclopeDIA: Library Searching Directly from Data-Independent Acquisition (DIA) MS/MS Data EncyclopeDIA Quantify 1.12.34+galaxy0 EncyclopeDIA Quantify: samples from Data-Independent Acquisition (DIA) MS/MS Data
enrichm			enrichm										0.6.5
ensembl-vep			ensembl-vep								106.1
ete3	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		ete3	Phylogenetics							3.1.3
EtherCalc			ethercalc						EtherCalc 0.1
eupathdb	Integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. The database portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera.		eupathdb	Model organisms Model organisms Zoology Gene transcripts	EuPathDB: A portal to eukaryotic pathogen databases				EuPathDB 1.0.0
ExaBayes	ExaBayes is a software package for Bayesian phylogenetic tree inference. It is particularly suitable for large-scale analyses on computer clusters.		exabayes	Phylogenetics			GPL-3.0					1.5.1
ExaML	Tool for phylogenomic analyses on supercomputers.		examl	Phylogeny Phylogenomics Literature and language	ExaML version 3: A tool for phylogenomic analyses on supercomputers		GPL-3.0					3.0.22
Exonerate	A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment.		exonerate	Sequence analysis Sequence sites, features and motifs Molecular interactions, pathways and networks	Automated generation of heuristics for biological sequence comparison	Exonerate	GPL-3.0		Exonerate 2.4.0+galaxy2		2.2.02.4.0 2.2.02.4.0		2.4.0--hf34a1b8_7
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.		export2graphlan	Taxonomy Metabolomics Biomarkers	Compact graphical representation of phylogenetic data and metadata with GraPhlAn		MIT		Export to GraPhlAn 0.20+galaxy0
export_remote			export_remote						Export datasets 0.1.0
eXpress	Streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It can be used to resolve ambiguous mappings in other high-throughput sequencing based applications.		eXpress	Gene expression Metagenomics RNA-seq ChIP-seq	2 publications Publications Improving RNA-Seq expression estimates by correcting for fragment bias 10.7490/f1000research.1114334.1		Apache-2.0		eXpress 1.1.1
Extract values from an SD-file			sdf_to_tab						Extract values from an SD-file 2020.03.4+galaxy0
f5c	GPU Accelerated Adaptive Banded Event Alignment for Rapid Comparative Nanopore Signal Analysis | Re-engineered and optimised Nanopolish call-methylation module (supports CUDA acceleration) | An optimised re-implementation of the call-methylation module in Nanopolish. Given a set of basecalled Nanopore reads and the raw signals, f5c detects the methylated cytosine bases. f5c can optionally utilise NVIDIA graphics cards for acceleration		f5c	Computer science Epigenetics Whole genome sequencing	2 publications Publications 10.1101/756122 GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis		MIT				1.3		1.1--h0326b38_1
Falcon (pb-assembly)	Experimental PacBio diploid assembler.		pb-assembly	Sequence assembly	10.5281/zenodo.35745								0.0.8--hdfd78af_1
fasta_compute_length	Add length of sequence to fasta header.		fasta_compute_length	Nucleic acids Sequence analysis Data management	2 publications Publications The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update 10.7490/f1000research.1114334.1				Compute sequence length 1.0.3
fastahack			fastahack										1.0.0-gcccore-10.3.0
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.		fastani	Microbiology Genetic variation			Apache-2.0						1.33-gcc-10.3.0
fastool	Read huge FastQ and FastA files (both normal and gzipped) an demanipulate them.		fastool	Data management			MIT						0.1.4--h7132678_6
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.		fastp	Sequence analysis Probes and primers	10.1093/bioinformatics/bty560	fastp	MIT		fastp 0.23.4+galaxy1	0.20.0			0.23.2-gcc-11.3.0
FASTQC	This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.		fastqc	Sequencing Data quality management Sequence analysis	10.7490/f1000research.1114334.1	FASTQC	GPL-3.0		FastQC 0.74+galaxy1	0.11.7	0.12.1	0.11.9--hdfd78af_1	0.11.9-java-11
fastqe	Compute quality stats for FASTQ files and print those stats as emoji... for some reason.		fastqe	Sequence analysis Sequencing					FASTQE 0.3.1+galaxy0
FastTree	Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.		fasttree	Phylogenetics Sequence analysis	2 publications Publications 10.1093/molbev/msp077 10.1371/journal.pone.0009490	FastTree			FASTTREE 2.1.10+galaxy1		2.1.11		2.1.11-gcccore-10.3.0
FASTX-Toolkit	Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.		fastx	Sequence analysis	Comparison of DNA sequences with protein sequences	FASTX-Toolkit	AGPL-3.0		9 tools Tool Name Description Remove sequencing artifacts 1.0.1+galaxy2 Remove sequencing artifacts: Barcode Splitter 1.0.1+galaxy2 Barcode Splitter: Clip 1.0.3+galaxy2 Clip: adapter sequences Collapse 1.0.1+galaxy2 Collapse: sequences Rename sequences 0.0.14+galaxy2 Rename sequences: Reverse-Complement 1.0.2+galaxy2 Reverse-Complement: Trim sequences 1.0.2+galaxy2 Trim sequences: Draw nucleotides distribution chart 1.0.1+galaxy2 Draw nucleotides distribution chart: Compute quality statistics 1.0.1+galaxy2 Compute quality statistics:
FASTX-Toolkit	Collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.		fastx_toolkit	Sequence analysis	Comparison of DNA sequences with protein sequences		AGPL-3.0		5 tools Tool Name Description Length Distribution 1.0.1+galaxy2 Length Distribution: chart FASTA Width 1.0.1+galaxy2 FASTA Width: formatter RNA/DNA 1.0.2+galaxy2 RNA/DNA: converter Filter by quality 1.0.2+galaxy2 Filter by quality: Draw quality score boxplot 1.0.1+galaxy2 Draw quality score boxplot:
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.		featurecounts	RNA-Seq	FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features		GPL-3.0		featureCounts 2.0.3+galaxy2
FEELnc	A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts.		feelnc	RNA-seq Functional, regulatory and non-coding RNA	FEELnc: A tool for long non-coding RNA annotation and its application to the dog transcriptome		GPL-3.0		FEELnc 0.2.1+galaxy0
fermi-lite			fermi-lite										20190320-gcccore-10.3.0
Fgenesh++	HMM-based gene structure prediction (multiple genes, both chains); Program for predicting multiple genes in genomic DNA sequences.		fgenesh	Gene structure	10.1186/gb-2006-7-s1-s10				FGENESH get protein 1.0.0+galaxy0
fgsea	The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.		fgsea	Genetics	10.1101/060012		MIT		fgsea 1.8.0+galaxy1
Filter Combined Transcripts			filter_transcripts_via_tracking						Filter Combined Transcripts 0.1
Filter pileup			pileup_parser						Filter pileup 1.0.2
Filter SAM			sam_bitwise_flag_filter						Filter SAM 1.0.0
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.		filtlong				GPL-3.0		filtlong 0.2.1+galaxy0
flashLFQ	FlashLFQ is an ultrafast label-free quantification algorithm for mass-spectrometry proteomics.		flashlfq	Proteomics experiment Proteomics			LGPL-3.0		FlashLFQ 1.0.3.1
flex			flex										2.6.4-gcccore-10.3.02.6.4-gcccore-11.3.02.6.4-gcccore-12.3.0 (D) 2.6.4-gcccore-10.3.02.6.4-gcccore-11.3.02.6.4-gcccore-12.3.0 (D) 2.6.4-gcccore-10.3.02.6.4-gcccore-11.3.02.6.4-gcccore-12.3.0 (D)
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.		flye	Sequence assembly Metagenomics Whole genome sequencing Genomics	3 publications Publications Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes Assembly of long, error-prone reads using repeat graphs metaFlye: scalable long-read metagenome assembly using repeat graphs				Flye 2.9.4+galaxy0		2.92.9.12.9.3 2.92.9.12.9.3 2.92.9.12.9.3		2.9-gcc-10.3.0
flymine	An integrated database for Drosophila and Anopheles genomics.		flymine	Data management Genomics Proteomics	2 publications Publications FlyMine: An integrated database for Drosophila and Anopheles genomics InterMine: A flexible data warehouse system for the integration and analysis of heterogeneous biological data		LGPL-2.1		Flymine 1.0.0
Foldseek	Foldseek enables fast and sensitive comparisons of large structure sets. It reaches sensitivities similar to state-of-the-art structural aligners while being at least 20,000 times faster.		foldseek	Proteins	2 publications Publications Fast and accurate protein structure search with Foldseek 10.1101/2022.02.07.479398		GPL-3.0				3-915ef7d
fpocket	Web server which detects small molecule pockets by relying on the geometric alpha sphere theory. It also tracks pockets during molecular dynamics so to provide insight on pocket dynamics (mdpocket) and transposes mdpocket to the combined analysis of homologous structures (hpocket).		fpocket	Protein structural motifs and surfaces	2 publications Publications fpocket: Online tools for protein ensemble pocket detection and tracking Fpocket: An open source platform for ligand pocket detection		Freeware		2 tools Tool Name Description dpocket 4.0.0+galaxy0 dpocket: to calculate descriptors for protein pockets fpocket 4.0.0+galaxy0 fpocket: - find potential binding sites in protein structures
FragGeneScan	Application for finding (fragmented) genes in short reads		fraggenescan	Genetics Sequence analysis	2 publications Publications FragGeneScan: Predicting genes in short and error-prone reads 10.7490/f1000research.1114334.1		GPL-3.0		FragGeneScan 1.30.0
freebayes	Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.		freebayes	Genomics Genetic variation Rare diseases		freebayes	MIT		2 tools Tool Name Description BamLeftAlign 1.3.6 BamLeftAlign: indels in BAM datasets FreeBayes 1.3.6+galaxy0 FreeBayes: bayesian genetic variant detector				1.3.6-foss-2021a-r-4.1.0
fsom			fsom										20141119-gcccore-10.3.0
funannotate	funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes).		funannotate	Genomics			BSD-2-Clause		5 tools Tool Name Description Funannotate predict annotation 1.8.15+galaxy5 Funannotate predict annotation: Sort assembly 1.8.15+galaxy5 Sort assembly: Funannotate assembly clean 1.8.15+galaxy5 Funannotate assembly clean: Funannotate functional 1.8.15+galaxy5 Funannotate functional: annotation Funannotate compare 1.8.15+galaxy4 Funannotate compare: annotations
gaeval	Gene Annotation EVAluation.		gaeval	Sequence analysis Gene structure			Not licensed		4 tools Tool Name Description AEGeAn CanonGFF3 0.16.0+galaxy1 AEGeAn CanonGFF3: pre-process GFF3 files, removing all features not directly related to protein-coding genes AEGeAn GAEVAL 0.16.0+galaxy1 AEGeAn GAEVAL: compute coverage and integrity scores for gene models using transcript alignments. AEGeAn LocusPocus 0.16.0+galaxy1 AEGeAn LocusPocus: calculate locus coordinates for the given gene annotation AEGeAn ParsEval 0.16.0+galaxy1 AEGeAn ParsEval: compare two sets of gene annotations for the same sequence.
Galaxy : Operate on Genomic Intervals			galaxy_genomic_intervals						2 tools Tool Name Description Intersect 1.0.0 Intersect: the intervals of two datasets Gene BED To Exon/Intron/Codon BED 1.0.0 Gene BED To Exon/Intron/Codon BED: expander
Galaxy text processing			text_processing						19 tools Tool Name Description Join 9.3+galaxy1 Join: two files Sort a row 9.3+galaxy1 Sort a row: according to their columns Text transformation 9.3+galaxy1 Text transformation: with sed Select first 9.3+galaxy1 Select first: lines from a dataset (head) Create text file 9.3+galaxy1 Create text file: with recurring lines Advanced Cut 9.3+galaxy2 Advanced Cut: columns from a table (cut) Concatenate datasets 9.3+galaxy1 Concatenate datasets: tail-to-head (cat) tac 9.3+galaxy1 tac: reverse a file (reverse cat) Unfold 9.3+galaxy1 Unfold: columns from a table Search in textfiles 9.3+galaxy1 Search in textfiles: (grep) Sort 9.3+galaxy1 Sort: data in ascending or descending order Replace Text 9.3+galaxy1 Replace Text: in entire line Replace Text 9.3+galaxy1 Replace Text: in a specific column Replace 9.3+galaxy1 Replace: parts of text Multi-Join 9.3+galaxy1 Multi-Join: (combine multiple files) Select last 9.3+galaxy1 Select last: lines from a dataset (tail) Unique 9.3+galaxy1 Unique: occurrences of each record Unique lines 9.3+galaxy1 Unique lines: assuming sorted input file Text reformatting 9.3+galaxy1 Text reformatting: with awk
Galaxy: Collection Operations			galaxy_collection_operations						19 tools Tool Name Description Split by group 0.6 Split by group: Split file 0.5.2 Split file: to dataset collection Bundle Collection 1.3.0 Bundle Collection: Package up and download a collection of files as a single archive. Collapse Collection 5.1.0 Collapse Collection: into single dataset in order of the collection Column join 0.0.3 Column join: on multiple datasets Unzip 6.0+galaxy0 Unzip: Unzip a file Unzip collection 1.0.0 Unzip collection: Zip collections 1.0.0 Zip collections: Filter failed datasets 1.0.0 Filter failed datasets: Filter empty datasets 1.0.0 Filter empty datasets: Flatten collection 1.0.0 Flatten collection: Merge collections 1.0.0 Merge collections: Relabel identifiers 1.0.0 Relabel identifiers: Filter collection 1.0.0 Filter collection: Sort collection 1.0.0 Sort collection: Tag elements 1.0.0 Tag elements: Apply rules 1.1.0 Apply rules: Build list 1.1.0 Build list: Extract dataset 1.0.1 Extract dataset:
Galaxy: Converters			Galaxy CONVERTER						75 tools Tool Name Description Genbank to GFF3 1.1 Genbank to GFF3: converter FASTA-to-Tabular 1.1.1 FASTA-to-Tabular: converter Create InterMine Interchange 0.0.1 Create InterMine Interchange: Dataset Tabular-to-FASTA 1.1.1 Tabular-to-FASTA: converts tabular file to FASTA format Convert VCF to MAF 1.6.21+galaxy1 Convert VCF to MAF: with vcf2maf BED-to-GFF 2.0.0 BED-to-GFF: converter MAF to BED 1.0.0 MAF to BED: Converts a MAF formatted file to the BED format MAF to Interval 1.0.0 MAF to Interval: Converts a MAF formatted file to the Interval format MAF to FASTA 1.0.1 MAF to FASTA: Converts a MAF formatted file to FASTA format SFF converter 1.0.1 SFF converter: AXT to concatenated FASTA 1.0.0 AXT to concatenated FASTA: Converts an AXT formatted file to a concatenated FASTA alignment AXT to FASTA 1.0.0 AXT to FASTA: Converts an AXT formatted file to FASTA format AXT to LAV 1.0.0 AXT to LAV: Converts an AXT formatted file to LAV format LAV to BED 1.0.0 LAV to BED: Converts a LAV formatted file to BED format Convert SAM to BAM without sorting 1.0.1 Convert SAM to BAM without sorting: Convert FASTQ files to seek locations 1.0.1 Convert FASTQ files to seek locations: Convert Wiggle to BigWig 1.0.1 Convert Wiggle to BigWig: Convert GRO to PDB 1.0.0 Convert GRO to PDB: Convert uncompressed file to compressed 1.16+galaxy0 Convert uncompressed file to compressed: Convert Interval to BGZIP 1.0.3 Convert Interval to BGZIP: Convert BAM to coordinate-sorted BAM 1.0.1 Convert BAM to coordinate-sorted BAM: Convert BAM to BigWig 1.0.2 Convert BAM to BigWig: OpenBabel converter for molecular formats 2.4.1 OpenBabel converter for molecular formats: Convert Picard Interval List to BED6 1.0.1 Convert Picard Interval List to BED6: converter Convert tabular to CSV 1.0.0 Convert tabular to CSV: Convert compressed file to uncompressed. 1.0.1 Convert compressed file to uncompressed.: Convert Genomic Intervals To Strict BED12 1.0.0 Convert Genomic Intervals To Strict BED12: Convert MAF to Genomic Intervals 1.0.3 Convert MAF to Genomic Intervals: Convert XTC, DCD, and TRR 1.0.0 Convert XTC, DCD, and TRR: Convert lped to plink pbed 0.02 Convert lped to plink pbed: Convert BED, GFF, or VCF to BigWig 1.0.1 Convert BED, GFF, or VCF to BigWig: Convert CML to SMILES 2.4.1 Convert CML to SMILES: Convert compressed file to uncompressed. 1.0.0 Convert compressed file to uncompressed.: Convert FASTA to Tabular 1.0.1 Convert FASTA to Tabular: Convert Interval to tabix 1.0.2 Convert Interval to tabix: Convert Len file to Linecount 1.0.1 Convert Len file to Linecount: Convert MOL2 to MOL 2.4.1 Convert MOL2 to MOL: Convert SMILES to MOL 2.4.1 Convert SMILES to MOL: Convert GFF to Interval Index 1.0.1 Convert GFF to Interval Index: Convert InChI to MOL 2.4.1 Convert InChI to MOL: Convert BigWig to Wiggle 377+galaxy0 Convert BigWig to Wiggle: Convert bigWig to wig Convert compressed and uncompressed BCF files 0.0.1 Convert compressed and uncompressed BCF files: Convert Ref taxonomy to Seq Taxonomy 1.0.1 Convert Ref taxonomy to Seq Taxonomy: converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format Convert tar to directory 1.0.1 Convert tar to directory: Convert Genomic Intervals To BED 1.0.0 Convert Genomic Intervals To BED: Convert SAM to BigWig 1.0.3 Convert SAM to BigWig: Convert BAM to queryname-sorted BAM 1.0.1 Convert BAM to queryname-sorted BAM: Convert FASTA to Bowtie base space Index 1.3.1 Convert FASTA to Bowtie base space Index: Convert plink pbed to ld reduced format 0.02 Convert plink pbed to ld reduced format: Convert FASTA to fai file 1.0.1 Convert FASTA to fai file: Convert BGZ VCF to tabix 1.0.2 Convert BGZ VCF to tabix: Convert neostore.zip files to neostore 1.0.0 Convert neostore.zip files to neostore: Convert plink pbed to linkage lped 0.02 Convert plink pbed to linkage lped: Convert BedGraph to BigWig 1.0.1 Convert BedGraph to BigWig: SMILES to SMILES 2.4.1 SMILES to SMILES: Convert Wiggle to Interval 1.0.1 Convert Wiggle to Interval: Convert MAF to Fasta 1.0.2 Convert MAF to Fasta: Convert FASTA to Bowtie color space Index 1.2.3 Convert FASTA to Bowtie color space Index: Convert Genomic Intervals To Strict BED6 1.0.1 Convert Genomic Intervals To Strict BED6: Convert Genomic Intervals To Coverage 1.0.1 Convert Genomic Intervals To Coverage: Convert GFF to Feature Location Index 1.0.0 Convert GFF to Feature Location Index: Convert PDB to GRO 1.0.0 Convert PDB to GRO: Convert CRAM to BAM 1.0.2 Convert CRAM to BAM: Convert FASTA to 2bit 1.0.1 Convert FASTA to 2bit: Convert BED to Feature Location Index 1.0.0 Convert BED to Feature Location Index: Convert Biom datasets 2.1.5 Convert Biom datasets: Convert Bam to Bai 1.0.1 Convert Bam to Bai: Convert CSV to tabular 1.0.0 Convert CSV to tabular: Convert tabular to dbnsfp 1.0.2 Convert tabular to dbnsfp: Convert Parquet to csv 1.0.0 Convert Parquet to csv: Convert GFF to BED 1.0.1 Convert GFF to BED: Convert lped to fped 0.02 Convert lped to fped: Convert BED to GFF 2.0.1 Convert BED to GFF: Convert FASTA to len file 1.0.1 Convert FASTA to len file: Convert Genomic Intervals To Strict BED 1.0.1 Convert Genomic Intervals To Strict BED:
Galaxy: Data sources			galaxy_data_sources						11 tools Tool Name Description EGA Download Client 5.0.2+galaxy0 EGA Download Client: UCSC Main 1.0.0 UCSC Main: table browser UCSC Archaea 1.0.0 UCSC Archaea: table browser SRA 1.0.1 SRA: server EBI SRA 1.0.1 EBI SRA: ENA SRA modENCODE fly 1.0.1 modENCODE fly: server modENCODE modMine 1.0.0 modENCODE modMine: server Ratmine 1.0.0 Ratmine: server modENCODE worm 1.0.1 modENCODE worm: server metabolicMine 1.0.0 metabolicMine: server EBI SCXA Data Retrieval v0.0.2+galaxy2 EBI SCXA Data Retrieval: Retrieves expression matrixes and metadata from EBI Single Cell Expression Atlas (SCXA)
Galaxy: Fetch Alignments/Sequences			galaxy_fetch_alignments_sequences						12 tools Tool Name Description Extract Pairwise MAF blocks 1.0.1 Extract Pairwise MAF blocks: given a set of genomic intervals Extract MAF blocks 1.0.1 Extract MAF blocks: given a set of genomic intervals Split MAF blocks 1.0.0 Split MAF blocks: by Species Stitch MAF blocks 1.0.1 Stitch MAF blocks: given a set of genomic intervals Stitch Gene blocks 1.0.1 Stitch Gene blocks: given a set of coding exon intervals MAF Coverage Stats 1.0.1 MAF Coverage Stats: Alignment coverage information Join MAF blocks 1.0.0 Join MAF blocks: by Species Filter MAF blocks 1.0.0 Filter MAF blocks: by Species Filter MAF blocks 1.0.1 Filter MAF blocks: by Size Extract MAF by block number 1.0.1 Extract MAF by block number: given a set of block numbers and a MAF file Reverse Complement 1.0.1 Reverse Complement: a MAF file Filter MAF 1.0.1 Filter MAF: by specified attributes
Galaxy: Filter and Sort			galaxy_filter_and_sort						10 tools Tool Name Description Sub-sample sequences files 0.2.6 Sub-sample sequences files: e.g. to reduce coverage Filter sequences by ID 0.2.9 Filter sequences by ID: from a tabular file Filter FASTA 2.3 Filter FASTA: on the headers and/or the sequences Filter 1.1.1 Filter: data on any column using simple expressions Sort 1.2.0 Sort: data in ascending or descending order Select 1.0.4 Select: lines that match an expression Extract features 1.0.0 Extract features: from GFF data Filter GFF data by attribute 0.2 Filter GFF data by attribute: using simple expressions Filter GFF data by feature count 0.1.1 Filter GFF data by feature count: using simple expressions Filter GTF data by attribute values_list 0.2 Filter GTF data by attribute values_list:
Galaxy: Graph/Display Data			galaxy_graph_display						11 tools Tool Name Description Plot confusion matrix, precision, recall and ROC and AUC curves 0.4 Plot confusion matrix, precision, recall and ROC and AUC curves: of tabular data Volcano Plot 0.0.6 Volcano Plot: create a volcano plot Draw Stacked Bar Plots 1.0.0 Draw Stacked Bar Plots: for different categories and different criteria Histogram 1.0.4 Histogram: of a numeric column Parallel Coordinates Plot 0.2 Parallel Coordinates Plot: of tabular data Plot actual vs predicted curves and residual plots 0.1 Plot actual vs predicted curves and residual plots: of tabular data proportional venn 0.5 proportional venn: from 2-3 sets Plotting tool 1.0.2 Plotting tool: for multiple series and graph types VCF to MAF Custom Track 1.0.1 VCF to MAF Custom Track: for display at UCSC Bar chart 1.0.0 Bar chart: for multiple columns Boxplot 1.0.1 Boxplot: of quality statistics
Galaxy: Join, Subtract and Group			galaxy_join_subtract_and_group						5 tools Tool Name Description Reverse 1.8+galaxy0 Reverse: columns in a tabular file Transpose 1.8+galaxy1 Transpose: rows/columns in a tabular file Join two Datasets 2.1.3 Join two Datasets: side by side on a specified field Compare two Datasets 1.0.2 Compare two Datasets: to find common or distinct rows Group 2.1.4 Group: data by a column and perform aggregate operation on other columns.
Galaxy: Sequence Utilities			galaxy_sequence_utils						21 tools Tool Name Description Concatenate 0.0.1 Concatenate: FASTA alignment by species Filter sequences by length 1.2 Filter sequences by length: FASTA Merge Files and Filter Unique Sequences 1.2.0 FASTA Merge Files and Filter Unique Sequences: Concatenate FASTA database files together Fasta Statistics 2.0 Fasta Statistics: display summary statistics for a FASTA file Combine FASTA and QUAL 1.1.5 Combine FASTA and QUAL: into FASTQ Filter FASTQ 1.1.5 Filter FASTQ: reads by quality score and length FASTQ Groomer 1.1.5 FASTQ Groomer: convert between various FASTQ quality formats Manipulate FASTQ 1.1.5 Manipulate FASTQ: reads on various attributes FASTQ Masker 1.1.5 FASTQ Masker: by quality score FASTQ de-interlacer 1.1.5 FASTQ de-interlacer: on paired end reads FASTQ interlacer 1.2.0.1+galaxy0 FASTQ interlacer: on paired end reads FASTQ joiner 2.0.1.1+galaxy0 FASTQ joiner: on paired end reads FASTQ splitter 1.1.5+galaxy1 FASTQ splitter: on joined paired end reads Quality format converter 1.0.1+galaxy2 Quality format converter: (ASCII-Numeric) FASTQ Summary Statistics 1.1.5 FASTQ Summary Statistics: by column FASTQ to FASTA 1.1.5 FASTQ to FASTA: converter FASTQ Trimmer 1.1.5 FASTQ Trimmer: by column FASTQ Quality Trimmer 1.1.5 FASTQ Quality Trimmer: by sliding window FASTQ to FASTA 1.0.2+galaxy2 FASTQ to FASTA: converter from FASTX-toolkit FASTQ to Tabular 1.1.5 FASTQ to Tabular: converter Tabular to FASTQ 1.1.5 Tabular to FASTQ: converter
Galaxy: Statistics			galaxy_statistics						8 tools Tool Name Description Categorize Elements 1.0.0 Categorize Elements: satisfying criteria Compute Motif Frequencies For All Motifs 1.0.0 Compute Motif Frequencies For All Motifs: motif by motif Compute Motif Frequencies 1.0.0 Compute Motif Frequencies: in indel flanking regions Correlation 1.0.0 Correlation: for numeric columns Count GFF Features 0.2 Count GFF Features: Row Means 0.1 Row Means: Calculates the mean of a row of numbers for an entire table T Test for Two Samples 1.0.1 T Test for Two Samples: Summary Statistics 1.1.2 Summary Statistics: for any numerical column
Galaxy: Text Manipulation			galaxy_text_manipulation						36 tools Tool Name Description Add input name as column 0.2.0 Add input name as column: to an existing tabular file SQLite to tabular 3.2.1 SQLite to tabular: for SQL query Filter Tabular 3.3.1 Filter Tabular: Number lines 9.3+galaxy1 Number lines: Column Regex Find And Replace 1.0.3 Column Regex Find And Replace: Regex Find And Replace 1.0.3 Regex Find And Replace: Add column 1.0.1 Add column: to an existing dataset Extract element identifiers 0.0.2 Extract element identifiers: of a list collection Column arrange 0.2 Column arrange: by header name Compute 2.0 Compute: on rows Concatenate multiple datasets 0.2 Concatenate multiple datasets: tail-to-head Concatenate multiple datasets 1.0 Concatenate multiple datasets: tail-to-head by specifying how Condense 1.0.0 Condense: consecutive characters cut_francais 1.0 cut_francais: keep or remove selected column Join two files 1.0.1 Join two files: on column allowing a small difference Replace column 0.2 Replace column: by values which are defined in a convert file Replace column 0.2 Replace column: by values which are defined in a convert file Table Compute 1.2.4+galaxy0 Table Compute: computes operations on table data Add column 1.0.0 Add column: to an existing dataset Concatenate datasets 1.0.0 Concatenate datasets: tail-to-head Cut 1.0.2 Cut: columns from a table Merge Columns 1.0.1 Merge Columns: together Convert 1.0.0 Convert: delimiters to TAB Create single interval 1.0.0 Create single interval: as a new dataset Change Case 1.0.0 Change Case: of selected columns Paste 1.0.0 Paste: two files side by side Remove beginning 1.0.0 Remove beginning: of a file Select random lines 2.0.2 Select random lines: from a file Select first 1.0.2 Select first: lines from a dataset Select last 1.0.1 Select last: lines from a dataset Trim 0.0.2 Trim: leading or trailing characters Line/Word/Character count 1.0.0 Line/Word/Character count: of a dataset Secure Hash / Message Digest 0.0.2 Secure Hash / Message Digest: on a dataset Add line to file 0.1.0 Add line to file: writes a line of text at the begining or end of a text file. Remove columns 1.0 Remove columns: by heading Pick parameter value 0.2.0 Pick parameter value:
GATK	The Genome Analysis Toolkit (GATK) is a set of bioinformatic tools for analyzing high-throughput sequencing (HTS) and variant call format (VCF) data. The toolkit is well established for germline short variant discovery from whole genome and exome sequencing data. GATK4 expands functionality into copy number and somatic analyses and offers pipeline scripts for workflows. Version 4 (GATK4) is open-source at https://github.com/broadinstitute/gatk.		gatk	Sequence analysis Genetic variation Sequencing Workflows	The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data	GATK				4.1.4.0 4.2.1.0 4.1.8.1 4.2.5.0		4.2.5.0--hdfd78af_0	4.3.0.0-gcccore-11.3.0-java-11
gblocks	Cleaning aligned sequences.		gblock	Sequence analysis	2 publications Publications Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis				Gblocks 0.91b
gcta	Genome-wide Complex Trait Analysis. Estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits.		gcta	GWAS study	GCTA: A tool for genome-wide complex trait analysis	gcta	MIT						1.94.0beta-gfbf-2022a1.94.1--h9ee0642_0 1.94.0beta-gfbf-2022a1.94.1--h9ee0642_0
gecko	Software aimed at pairwise sequence comparison generating high quality results (equivalent to MUMmer) with controlled memory consumption and comparable or faster execution times particularly with long sequences.		gecko	Sequence analysis	Breaking the computational barriers of pairwise genome comparison		GPL-3.0		Gecko 1.2
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.		gemini	Sequence analysis	10.1371/journal.pcbi.1003153		MIT		24 tools Tool Name Description GEMINI actionable_mutations 0.20.1 GEMINI actionable_mutations: Retrieve genes with actionable somatic mutations via COSMIC and DGIdb GEMINI amend 0.20.1 GEMINI amend: Amend an already loaded GEMINI database. GEMINI annotate 0.20.1+galaxy2 GEMINI annotate: the variants in an existing GEMINI database with additional information GEMINI burden 0.20.1 GEMINI burden: perform sample-wise gene-level burden calculations GEMINI comp_hets 0.18.1.1 GEMINI comp_hets: Identifying potential compound heterozygotes GEMINI database info 0.20.1 GEMINI database info: Retrieve information about tables, columns and annotation data stored in a GEMINI database GEMINI de_novo 0.18.1.1 GEMINI de_novo: Identifying potential de novo mutations GEMINI dump 0.18.1.1 GEMINI dump: Extract data from the Gemini DB GEMINI fusions 0.20.1 GEMINI fusions: Identify somatic fusion genes from a GEMINI database GEMINI gene_wise 0.20.1 GEMINI gene_wise: Discover per-gene variant patterns across families GEMINI inheritance pattern 0.20.1 GEMINI inheritance pattern: based identification of candidate genes GEMINI interactions 0.20.1 GEMINI interactions: Find genes among variants that are interacting partners GEMINI load 0.20.1+galaxy2 GEMINI load: Loading a VCF file into GEMINI GEMINI lof_sieve 0.20.1 GEMINI lof_sieve: Filter LoF variants by transcript position and type GEMINI mendel_errors 0.18.1.1 GEMINI mendel_errors: Identify candidate violations of Mendelian inheritance GEMINI pathways 0.20.1 GEMINI pathways: Map genes and variants to KEGG pathways GEMINI qc 0.20.1 GEMINI qc: Quality control tool GEMINI query 0.20.1+galaxy1 GEMINI query: Querying the GEMINI database GEMINI autosomal recessive/dominant 0.18.1.1 GEMINI autosomal recessive/dominant: Find variants meeting an autosomal recessive/dominant model GEMINI region 0.18.1.1 GEMINI region: Extracting variants from specific regions or genes GEMINI roh 0.20.1 GEMINI roh: Identifying runs of homozygosity GEMINI set_somatic 0.20.1 GEMINI set_somatic: Tag somatic mutations in a GEMINI database GEMINI stats 0.20.1 GEMINI stats: Compute useful variant statistics GEMINI windower 0.20.1 GEMINI windower: Compute sliding window statistics from variants
gemoma	Gene Model Mapper is a homology-based gene prediction program. GeMoMa uses the annotation of protein-coding genes in a reference genome to infer the annotation of protein-coding genes in a target genome. Thereby, it utilizes amino acid sequence and intron position conservation. In addition, it allows to incorporate RNA-seq evidence for splice site prediction.		gemoma	Genomics Homology modeling	Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi		GPL-3.0				1.81.9 1.81.9
geneiobio	An interactive web tool for versatile, clinically-driven variant interrogation and prioritization. IOBIO is a suite of web apps for visually driven real-time analysis of genomic data. Visually driven real-time analysis of genomic data.		geneiobio	Exome sequencing Genomics Medicine Genetic variation Genotype and phenotype	10.1101/2020.11.05.20224865				gene.iobio visualisation 4.7.1+galaxy1
generate_count_matrix			generate_count_matrix						Generate count matrix 1.0
generate_pc_lda_matrix			generate_pc_lda_matrix						Generate A Matrix 1.0.0
generode			generode								0.5.1
GenomeScope	Reference-free profiling of polyploid genomes | We have developed GenomeScope 2.0, which applies classical insights from combinatorial theory to establish a detailed mathematical model of how k-mer frequencies will be distributed in heterozygous and polyploid genomes | Average k-mer coverage for polyploid genome | Upload results from running Jellyfish or KMC		genomescope	Sequence assembly Mathematics Mapping	10.1101/747568		Apache-2.0		GenomeScope 2.0.1+galaxy0		1.0.01.0.0 1.0.01.0.0
GenomeTools	Free collection of bioinformatics tools for genome informatics.		genometools	Nucleic acid sites, features and motifs Sequence analysis	Genome tools: A comprehensive software library for efficient processing of structured genome annotations	GenomeTools	BSD-3-Clause				1.6.2
genrich			genrich						Genrich 0.5+galaxy2
get_pdb_file			get_pdb_file						Get PDB file 0.1.0
getorganelle	A fast and versatile toolkit for accurate de novo assembly of organelle genomes. This toolkit assemblies organelle genome from genomic skimming data.		getorganelle	Cell biology Sequence assembly Whole genome sequencing Plant biology Model organisms	GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes		GPL-3.0		2 tools Tool Name Description Get organelle from reads 1.7.7.1+galaxy0 Get organelle from reads: Get annotated regions from genbank files (getorganelle) 0.1.0 Get annotated regions from genbank files (getorganelle):
gfa_to_fa			gfa_to_fa						GFA to FASTA 0.1.2
gfastats	gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless fasta/fastq/gfa conversion.		gfastats	Computational biology			MIT		gfastats 1.3.6+galaxy0		1.3.6
gff2bed1			gff2bed1						GFF-to-BED 1.0.1
gff3sort			gff3sort										0.1.a1a2bc9--hdfd78af_2
gffcompare	Program for comparing, annotating, merging and tracking transcripts in GFF files.		gffcompare	Nucleic acids Sequence analysis			MIT		GffCompare 0.12.6+galaxy0				0.12.2-gcc-10.3.0
gffcompare_to_bed			gffcompare_to_bed						Convert gffCompare annotated GTF to BED 0.2.1
gffread	program for filtering, converting and manipulating GFF files		gffread	Nucleic acids Sequence analysis			MIT		gffread 2.2.1.4+galaxy0		0.12.7		0.12.7-gcccore-10.3.0
ggplot2	Plotting system for R, based on the grammar of graphics.		ggplot2	Data visualisation	10.1007/978-3-319-24277-4				6 tools Tool Name Description heatmap2 3.1.3.1+galaxy0 heatmap2: Histogram with ggplot2 3.4.0+galaxy0 Histogram with ggplot2: Heatmap w ggplot 3.4.0+galaxy0 Heatmap w ggplot: Scatterplot with ggplot2 3.4.0+galaxy1 Scatterplot with ggplot2: PCA plot w ggplot2 3.4.0+galaxy0 PCA plot w ggplot2: Violin plot w ggplot2 3.4.0+galaxy0 Violin plot w ggplot2:
ghostscript			ghostscript										9.54.0-gcccore-10.3.09.56.1-gcccore-11.3.0 (D) 9.54.0-gcccore-10.3.09.56.1-gcccore-11.3.0 (D)
GMAJ			GMAJ						GMAJ 2.0.1
gmap	Genomic Mapping and Alignment Program for mRNA and EST Sequences.		gmap	Mapping	2 publications Publications GMAP: A genomic mapping and alignment program for mRNA and EST sequences 10.7490/f1000research.1114334.1	gmap							2023.04.28
GNU parallel	GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. The typical input is a list of files, a list of hosts, a list of users, a list of URLs, or a list of tables. A job can also be a command that reads from a pipe. GNU parallel can then split the input and pipe it into commands in parallel.		parallel				GPL-3.0			20191022			20210622-gcccore-10.3.020220722-gcccore-11.3.0 (D) 20210622-gcccore-10.3.020220722-gcccore-11.3.0 (D)
GNU scientific library	The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.		gsl				GPL-3.0			2.6			2.7-gcc-10.3.02.7-gcc-11.3.0 (D) 2.7-gcc-10.3.02.7-gcc-11.3.0 (D)
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.		goenrichment	Transcriptomics			Apache-2.0		2 tools Tool Name Description GOEnrichment 2.0.1 GOEnrichment: performs GO enrichment analysis of a set of gene products GOSlimmer 1.0.1 GOSlimmer: converts a set of annotation from GO to a given GOSlim version
goseq	Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data.		goseq	RNA-Seq	10.1186/gb-2010-11-2-r14	goseq	GPL-2.0		goseq 1.50.0+galaxy0
gramenemart			gramenemart						GrameneMart 1.0.1
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.		graphlan	Metagenomics Phylogenetics Phylogenomics Cladistics	Compact graphical representation of phylogenetic data and metadata with GraPhlAn		MIT		2 tools Tool Name Description GraPhlAn 1.1.3 GraPhlAn: to produce graphical output of an input tree Generation, personalization and annotation of tree 1.1.3 Generation, personalization and annotation of tree: for GraPhlAn
Gromacs	Versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since it is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.		gromacs	Molecular dynamics	10 publications Publications Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers GROMACS: Fast, flexible, and free Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS Tackling exascale software challenges in molecular dynamics simulations with GROMACS GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit GRGMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation GROMACS 3.0: A package for molecular simulation and trajectory analysis GROMACS: A message-passing parallel molecular dynamics implementation Best bang for your buck: GPU nodes for GROMACS biomolecular simulations More bang for your buck: Improved use of GPU nodes for GROMACS 2018		LGPL-2.1		8 tools Tool Name Description Modify/convert and concatate GROMACS trajectories 2022+galaxy2 Modify/convert and concatate GROMACS trajectories: using trjconv and trjcat GROMACS structure configuration 2022+galaxy0 GROMACS structure configuration: using editconf GROMACS energy minimization 2022+galaxy0 GROMACS energy minimization: of the system prior to equilibration and production MD Extract energy components with GROMACS 2022+galaxy1 Extract energy components with GROMACS: Merge GROMACS topologies 3.4.3+galaxy0 Merge GROMACS topologies: and GRO files GROMACS initial setup 2022+galaxy0 GROMACS initial setup: of topology and GRO structure file GROMACS simulation 2022+galaxy0 GROMACS simulation: for system equilibration or data collection GROMACS solvation and adding ions 2022+galaxy0 GROMACS solvation and adding ions: to structure and topology files	2019.3 2019.3-plumed 2019.3-gpuvolta 2018.3 2018.3-plumed 2020.1 2020.1-plumed 2020.1-gpuvolta 2020.3 2020.3-gpuvolta 2021-gpuvolta 2021 2021.2 2021.2-gpuvolta 2021.4 2021.4-gpuvolta 2022 2022-gpuvolta 2020.3-gpuampere 2019.3-gpuampere 2021-gpuampere 2020.1-gpuampere 2021.2-gpuampere 2021.4-gpuampere 2022-gpuampere			2021.3-foss-2021a
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).		gtdb-tk	Metagenomics Taxonomy Phylogenetics Database management Proteins	GTDB-Tk: A toolkit to classify genomes with the genome taxonomy database		GPL-3.0		GTDB-Tk Classify genomes 2.3.2+galaxy1				2.0.0-foss-2021a2.2.6 2.0.0-foss-2021a2.2.6
gtf2bedgraph			gtf2bedgraph						GTF-to-BEDGraph 1.0.0
gtf2gene_list			gtf2gene_list						GTF2GeneList 1.52.0+galaxy0
gubbins	Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.		gubbins	Phylogeny Genotype and phenotype Whole genome sequencing	10.1093/nar/gku1196		GPL-2.0		Gubbins 3.2.1+galaxy0
gzip			gzip						Compress file(s) 0.1.0				1.10-gcccore-10.3.01.12-gcccore-11.3.0 (D) 1.10-gcccore-10.3.01.12-gcccore-11.3.0 (D)
hapcut2	HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy across a range of long- and short-read sequencing technologies. The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md		hapcut2						Hapcut2 1.3.3+galaxy0+ga1
hbvar			hbvar						HbVar 2.0.0
heinz	Tool for single-species active module discovery.		heinz	Genetics Gene expression Molecular interactions, pathways and networks	XHeinz: An algorithm for mining cross-species network modules under a flexible conservation model				4 tools Tool Name Description Calculate a Heinz score 1.0 Calculate a Heinz score: for each node Visualize 0.1.1 Visualize: the optimal scoring subnetwork Fit a BUM model 1.0 Fit a BUM model: with p-values Identify optimal scoring subnetwork 1.0 Identify optimal scoring subnetwork: using Heinz
Helixer	Deep Learning to predict gene annotations		helixer	Sequence analysis Gene transcripts	Helixer: Cross-species gene annotation of large eukaryotic genomes using deep learning		GPL-3.0		Helixer 0.3.2
hgv_david	This tool provides functional annotation for a list of genes by connecting with DAVID database.		hgv_david	Ontology and terminology Gene expression	3 publications Publications Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update 10.7490/f1000research.1114334.1				DAVID 1.0.1
hgv_ldtools	This tool can be used to analyze the patterns of linkage disequilibrium (LD) between polymorphic sites in a locus.		hgv_ldtools	Mapping Molecular interactions, pathways and networks DNA polymorphism Data mining	3 publications Publications Selecting a Maximally Informative Set of Single-Nucleotide Polymorphisms for Association Analyses Using Linkage Disequilibrium The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update 10.7490/f1000research.1114334.1				LD 1.0.0
hgv_linkToGProfile	This tool creates a link to the g:GOSt tool (Gene Group Functional Profiling), which provides functional profiling of gene lists.		hgv_linkToGProfile	Ontology and terminology Function analysis Data mining	3 publications Publications G:Profiler-a web-based toolset for functional profiling of gene lists from large-scale experiments The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update 10.7490/f1000research.1114334.1				g:Profiler 1.0.0
hicexplorer	A web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization. HiCExplorer — HiCExplorer 3.6 documentation. scHiCExplorer — scHiCExplorer 7 documentation. Free document hosting provided by Read the Docs.		hicexplorer	Workflows DNA Chromosome conformation capture ChIP-seq Epigenetics	Galaxy HiCExplorer 3: A web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization				57 tools Tool Name Description hicValidateLocations 3.7.5+galaxy0 hicValidateLocations: validate detected loops with protein peaks. hicTransform 3.7.5+galaxy0 hicTransform: transform a matrix to obs/exp, pearson and covariance matrices hicSumMatrices 3.7.5+galaxy0 hicSumMatrices: combine Hi-C matrices of the same size hicQuickQC 3.7.5+galaxy0 hicQuickQC: get a first quality estimate of Hi-C data hicPlotViewpoint 3.7.5+galaxy0 hicPlotViewpoint: plot interactions around a viewpoint hicPlotSVL 3.7.5+galaxy0 hicPlotSVL: plots the relation of short vs long range contacts hicPlotAverageRegions 3.7.5+galaxy0 hicPlotAverageRegions: plot the average regions from hicAverageRegions hicNormalize 3.7.5+galaxy0 hicNormalize: normalizes a matrix to norm range or smallest read count hicMergeLoops 3.7.5+galaxy0 hicMergeLoops: merge detected loops of different resolutions. hicInterIntraTAD 3.7.5+galaxy0 hicInterIntraTAD: computes the ratio of inter TAD-scores vs. intra TADs hicInfo 3.7.5+galaxy0 hicInfo: get information about the content of a Hi-C matrix hicHyperoptDetectLoops 3.7.5+galaxy0 hicHyperoptDetectLoops: optimizes parameters for hicDetectLoops hicFindRestSite 3.7.5+galaxy0 hicFindRestSite: identify restriction enzyme sites hicDifferentialTAD 3.7.5+galaxy0 hicDifferentialTAD: searches for differential TADs hicDetectLoops 3.7.5+galaxy0 hicDetectLoops: searches for enriched regions hicCorrelate 3.7.5+galaxy0 hicCorrelate: compute pairwise correlations between multiple Hi-C contact matrices hicCorrectMatrix 3.7.5+galaxy0 hicCorrectMatrix: run a Hi-C matrix correction algorithm hicCompartmentalization 3.7.5+galaxy0 hicCompartmentalization: compute pairwise correlations between multiple Hi-C contact matrices hicAverageRegions 3.7.5+galaxy0 hicAverageRegions: sums Hi-C contacts around given reference points and computes their average. hicAggregateContacts 3.7.5+galaxy0 hicAggregateContacts: allow plotting of aggregated Hi-C contacts between regions specified in a file hicAdjustMatrix 3.7.5+galaxy0 hicAdjustMatrix: adjust the shape of a Hi-C matrix chicViewpointBackgroundModel 3.7.5+galaxy0 chicViewpointBackgroundModel: compute a background model for cHi-C / HiChIP data chicViewpoint 3.7.5+galaxy0 chicViewpoint: computes viewpoints with the given reference points and a background model. chicSignificantInteractions 3.7.5+galaxy0 chicSignificantInteractions: computes viewpoints with the given reference points and a background model chicPlotViewpoint 3.7.5+galaxy0 chicPlotViewpoint: creates plots for viewpoints chicDifferentialTest 3.7.5+galaxy0 chicDifferentialTest: computes differential interactions of viewpoints chicAggregateStatistic 3.7.5+galaxy0 chicAggregateStatistic: computes with a target file the to be tested regions for chicDifferentialTest scHicQualityControl 4.1 scHicQualityControl: quality control for single-cell Hi-C interaction matrices scHicPlotClusterProfiles 4.1 scHicPlotClusterProfiles: plot single-cell Hi-C interaction matrices cluster profiles scHicMergeToSCool 4.1 scHicMergeToSCool: merge multiple cool files to one scool file scHicMergeMatrixBins 4.1 scHicMergeMatrixBins: change the resolution of the scHi-C matrices scHicInfo 4.1 scHicInfo: information about a single-cell scool matrix scHicDemultiplex 4.1 scHicDemultiplex: demultiplexes Nagano 2017 raw fastq files scHicCreateBulkMatrix 4.1 scHicCreateBulkMatrix: creates the bulk matrix out of single-cell Hi-C interaction matrices scHicCorrectMatrices 4.1 scHicCorrectMatrices: correct with KR algorithm single-cell Hi-C interaction matrices scHicConsensusMatrices 4.1 scHicConsensusMatrices: creates per cluster one average matrix scHicClusterSVL 4.1 scHicClusterSVL: clusters single-cell Hi-C interaction matrices with svl dimension reduction scHicClusterMinHash 4.1 scHicClusterMinHash: clusters single-cell Hi-C interaction matrices with MinHash dimension reduction scHicClusterCompartments 4.1 scHicClusterCompartments: clusters single-cell Hi-C interaction matrices with A/B compartments dimension reduction scHicAdjustMatrix 4.1 scHicAdjustMatrix: clusters single-cell Hi-C interaction matrices on the raw data hicTrainTADClassifier 3.7.2+galaxy0 hicTrainTADClassifier: train a TAD detection ML model hicPlotDistVsCounts 3.7.5+galaxy0 hicPlotDistVsCounts: compute distance vs Hi-C counts plot per chromosome hicMergeDomains 3.7.5+galaxy0 hicMergeDomains: Merges TAD domains hicConvertFormat 3.7.5+galaxy0 hicConvertFormat: Convert between different file formats hicCompareMatrices 3.7.5+galaxy0 hicCompareMatrices: normalize and compare two Hi-C contact matrices chicExportData 3.7.5+galaxy0 chicExportData: exports data of hdf to txt based files chicQualityControl 3.7.5+galaxy0 chicQualityControl: generates an estimate of the quality of each viewpoint hicTADClassifier 3.7.2+galaxy0 hicTADClassifier: TAD detection based on ML models scHicCluster 4.1 scHicCluster: clusters single-cell Hi-C interaction matrices on the raw data scHicNormalize 4.1 scHicNormalize: normalize single-cell Hi-C interaction matrices to the same read coverage scHicPlotConsensusMatrices 4.1 scHicPlotConsensusMatrices: plot single-cell Hi-C interaction matrices cluster consensus matrices hicPlotTADs 2.1.4.0 hicPlotTADs: plot Hi-C contact matrices heatmaps alongside other data tracks hicPlotMatrix 3.7.5+galaxy0 hicPlotMatrix: plot a Hi-C contact matrix heatmap hicPCA 3.7.5+galaxy0 hicPCA: compute the principal components for A / B compartment analysis hicMergeMatrixBins 3.7.5+galaxy0 hicMergeMatrixBins: merge adjacent bins from a Hi-C contact matrix to reduce its resolution hicFindTADs 3.7.5+galaxy0 hicFindTADs: identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin hicBuildMatrix 3.7.5+galaxy0 hicBuildMatrix: create a contact matrix
hifiadapterfilt	Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).		hifiadapterfilt	Sequence assembly Agricultural science Workflows Whole genome sequencing	HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly		GPL-3.0		HiFi Adapter Filter 2.0.0+galaxy0		2.0.0
hifiasm	Hifiasm: a haplotype-resolved assembler for accurate Hifi reads		hifiasm	Sequence assembly	Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm		MIT		Hifiasm 0.19.9+galaxy0		0.16.10.18.90.19.60.19.80.19.9 0.16.10.18.90.19.60.19.80.19.9 0.16.10.18.90.19.60.19.80.19.9 0.16.10.18.90.19.60.19.80.19.9 0.16.10.18.90.19.60.19.80.19.9		0.16.1-gcccore-10.3.0
hifiasm_meta	Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.		hifiasm_meta	Sequence assembly Metagenomics			MIT		Hifiasm_meta 0.3.1+galaxy0
HISAT2	Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).		hisat2	RNA-seq	3 publications Publications HISAT: A fast spliced aligner with low memory requirements Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown Simulation-based comprehensive benchmarking of RNA-seq aligners	HISAT2	GPL-3.0		HISAT2 2.2.1+galaxy1		2.2.1		2.2.1-gompi-2021a2.2.1-gompi-2022a2.2.1--h87f3376_4 2.2.1-gompi-2021a2.2.1-gompi-2022a2.2.1--h87f3376_4 2.2.1-gompi-2021a2.2.1-gompi-2022a2.2.1--h87f3376_4
hmmcleaner			hmmcleaner								0.180750
HMMER	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.		hmmer	Sequence analysis Sequence sites, features and motifs Gene and protein families	4 publications Publications HMMER web server: Interactive sequence similarity searching Accelerated profile HMM searches Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions HMMER web server: 2018 update		Other		12 tools Tool Name Description hmmconvert 0.1.0 hmmconvert: convert profile file to a HMMER format hmmalign 0.1.0 hmmalign: align sequences to a profile HMM phmmer 0.1.0 phmmer: search a protein sequence against a protein database (BLASTP-like) nhmmer 0.1.0 nhmmer: search a DNA model or alignment against a DNA database (BLASTN-like) alimask 0.1.0 alimask: append modelmask line to a multiple sequence alignments hmmscan 0.1.0 hmmscan: search sequence(s) against a profile database jackhmmer 0.1.0 jackhmmer: iteratively search a protein sequence against a protein database (PSIBLAST-like) hmmsearch 0.1.0 hmmsearch: search profile(s) against a sequence database nhmmscan 0.1.0 nhmmscan: search DNA sequence(s) against a DNA profile database hmmbuild 0.1.0 hmmbuild: Build a profile HMM from an input multiple alignment hmmfetch 0.1.0 hmmfetch: retrieve profile HMM(s) from a file hmmemit 0.1.0 hmmemit: sample sequence(s) from a profile HMM		3.3.2		3.3.2-gompi-2021a3.3.2-gompi-2022a (D) 3.3.2-gompi-2021a3.3.2-gompi-2022a (D)
horovod	Horovod is a distributed deep learning training framework for TensorFlow, Keras, PyTorch, and Apache MXNet. The goal of Horovod is to make distributed deep learning fast and easy to use.		horovod	Machine learning			Apache-2.0			0.19.0 0.22.1
HTSeq	Python framework to process and analyse high-throughput sequencing (HTS) data		htseq	Sequence analysis	HTSeq-A Python framework to work with high-throughput sequencing data	HTSeq	GPL-3.0		htseq-count 2.0.5+galaxy0				2.0.2-foss-2022a
HTSlib	The main purpose of HTSlib is to provide access to genomic information files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF and BCF formats). The library also provides interfaces to access and index genome reference data in FASTA format and tab-delimited files with genomic coordinates. It is utilized and incorporated into both SAMtools and BCFtools.		htslib	Data management	HTSlib: C library for reading/writing high-Throughput sequencing data	HTSlib	MIT			1.9 1.12 1.16	1.19.11.20 1.19.11.20		1.12-gcc-10.3.01.15.1-gcc-11.3.0 (D) 1.12-gcc-10.3.01.15.1-gcc-11.3.0 (D)
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)?”		humann	Metagenomics Phylogenomics	Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with biobakery 3		MIT		12 tools Tool Name Description Join (merge) 3.8+galaxy0 Join (merge): gene, pathway, or taxonomy HUMAnN/MetaPhlAn tables into a single table Make strain profiles 3.8+galaxy0 Make strain profiles: Split 3.8+galaxy0 Split: a merged HUMAnN table Reduce 3.8+galaxy0 Reduce: a joined HUMAnN table Barplot 3.8+galaxy0 Barplot: stratified HUMAnN features Regroup 3.8+galaxy0 Regroup: HUMAnN table features Renormalize 3.8+galaxy0 Renormalize: a HUMAnN generated table Split a HUMAnN table 3.8+galaxy0 Split a HUMAnN table: into 2 tables (one stratified and one unstratified) Unpack pathway abundances 3.8+galaxy0 Unpack pathway abundances: to show the genes for each HUMAnN 3.8+galaxy0 HUMAnN: to profile presence/absence and abundance of microbial pathways and gene families Rename features 3.8+galaxy0 Rename features: of a HUMAnN generated table Perform metadata association 3.8+galaxy0 Perform metadata association: on HUMAnN generated table				3.6-foss-2022a
HUMAnN2	HUMAnN 2.0 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 capable of doing)?”		humann2		Species-level functional profiling of metagenomes and metatranscriptomes				7 tools Tool Name Description Combine MetaPhlAn2 and HUMAnN2 outputs 0.2.0 Combine MetaPhlAn2 and HUMAnN2 outputs: to relate genus/species abundances and gene families/pathways abundances HUMAnN2 0.11.1.3 HUMAnN2: to profile presence/absence and abundance of microbial pathways and gene families Create a genus level gene families file 0.11.1.1 Create a genus level gene families file: Regroup 0.11.1.1 Regroup: a HUMAnN2 generated table by features Renormalize 0.11.1.1 Renormalize: a HUMAnN2 generated table Unpack pathway abundances to show genes included 0.11.1.1 Unpack pathway abundances to show genes included: Join 0.11.1.2 Join: HUMAnN2 generated tables
HybPiper	Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae). Recovering genes from targeted sequence capture data. Current version: 1.3.1 (August 2018). -- Read our article in Applications in Plant Sciences (Open Access). HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.		hybpiper	Phylogenetics Plant biology Gene transcripts Sequence assembly Phylogenomics	10.1101/854232		GPL-3.0		HybPiper 2.1.6+galaxy0
HyPhy	Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.		HyPhy	Phylogeny Small molecules Molecular interactions, pathways and networks	2 publications Publications 10.1007/978-1-4939-8736-8_6 10.1093/bioinformatics/bti079		Unlicense		2 tools Tool Name Description HyPhy-aBSREL 2.5.47+galaxy0 HyPhy-aBSREL: adaptive Branch Site Random Effects Likelihood HyPhy-GARD 2.5.47+galaxy0 HyPhy-GARD: Genetic Algorithm for Recombination Detection
IDL			idl							8.6 8.8
ImageMagick			imagemagick							7.0.11			7.0.11-14-gcccore-10.3.07.1.0-37-gcccore-11.3.0 (D) 7.0.11-14-gcccore-10.3.07.1.0-37-gcccore-11.3.0 (D)
Improved Phased Assembler (pbipa)	Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies		pbipa	Sequence assembly							1.5.01.8.0 1.5.01.8.0
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.		infernal	Sequence sites, features and motifs Structural genomics	Infernal 1.1: 100-fold faster RNA homology searches		BSD-3-Clause		6 tools Tool Name Description cmscan 1.1.4+galaxy0 cmscan: Search sequences against collections of covariance models cmalign 1.1.4+galaxy0 cmalign: Align sequences to a covariance model against a sequence database cmsearch 1.1.4+galaxy0 cmsearch: Search covariance model(s) against a sequence database cmpress 1.1.4+galaxy0 cmpress: Prepare a covariance model database for cmscan cmbuild 1.1.4+galaxy0 cmbuild: Build covariance models from sequence alignments cmstat 1.1.4+galaxy0 cmstat: Summary statistics for covariance model
insight-toolkit			insight-toolkit							5.2.1
Integrated Genomics Viewer	High-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types and format, including short-read alignments in the SAM/BAM format. Data can be viewed from local files or over the web via http.		igv	Genomics Data visualisation Sequence analysis	3 publications Publications Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration Integrative genomics viewer igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)	Integrated Genomics Viewer	LGPL-2.1			2.13.1
integron_finder	A tool to detect Integron in DNA sequences.		integron_finder	Functional genomics Mobile genetic elements Molecular biology Sequence analysis	2 publications Publications Identification and analysis of integrons and cassette arrays in bacterial genomes Integron Functionality and Genome Innovation: An Update on the Subtle and Smart Strategy of Integrase and Gene Cassette Expression Regulation		GPL-3.0		Integron Finder 2.0.5+galaxy0
intermine	Open source data warehouse built specifically for the integration and analysis of complex biological data. It enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding your own data.		intermine	Data integration and warehousing Rare diseases	2 publications Publications InterMine: A flexible data warehouse system for the integration and analysis of heterogeneous biological data InterMine: Extensive web services for modern biology		LGPL-2.1		InterMine 1.0.0
InterProScan	Scan sequences against the InterPro protein signature databases.		interproscan	Gene and protein families Sequence analysis	2 publications Publications InterProScan 5: Genome-scale protein function classification Search and sequence analysis tools services from EMBL-EBI in 2022				InterProScan 5.59-91.0+galaxy3				5.55-88.0-foss-2021a
ipyrad	Interactive assembly and analysis of RADseq datasets. ipyrad: interactive assembly and analysis of RAD-seq data sets. Welcome to ipyrad, an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies. Welcome to ipyrad — ipyrad documentation.		ipyrad	Sequence assembly Phylogenetics Population genetics	Ipyrad: Interactive assembly and analysis of RADseq datasets		GPL-3.0				0.9.84		0.9.93
IQ-TREE	Very efficient phylogenetic software for reconstructing maximum-likelihood trees and assessing branch supports with the ultrafast bootstrap approximation. It is based on the IQPNNI algorithm with 10-fold speedup together with substantially additional features.		iq-tree	Phylogenetics Statistics and probability Phylogenomics	W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis				IQ-TREE 2.3.6+galaxy0		2.1.2		2.2.2.3--h2202e69_2
iSEE	Provides functions for creating an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. Particular attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.		isee	Gene expression Transcriptomics	iSEE: Interactive SummarizedExperiment Explorer [version 1; referees: 2 approved]	iSEE	MIT		iSEE 1.0.0
ISEScan	Automated identification of insertion sequence elements in prokaryotic genomes.		isescan	Genomics DNA structural variation Sequence analysis Genetic variation	ISEScan: automated identification of insertion sequence elements in prokaryotic genomes				ISEScan 1.7.2.3+galaxy1
IsoformSwitchAnalyzeR	Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well.		isoformswitchanalyzer	Computational biology Gene transcripts	The landscape of isoform switches in human cancers		GPL-2.0		IsoformSwitchAnalyzeR 1.20.0+galaxy5
IsoSeq3	IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application. A composable workflow of existing tools and algorithms, combined with a new clustering technique.		isoseq3	Gene transcripts			BSD-3-Clause-Clear						4.0.0--h9ee0642_0
ivar	Interpretation-oriented tool to manage the update and revision of variant annotation and classification. iVar - DataBase of Genomics Variants.		ivar	Biological databases Evolutionary biology Sequencing	10.22541/AU.160610419.99549785/V1		AGPL-3.0		6 tools Tool Name Description ivar trim 1.4.3+galaxy0 ivar trim: Trim reads in aligned BAM ivar variants 1.4.3+galaxy1 ivar variants: Call variants from aligned BAM file ivar filtervariants 1.4.3+galaxy0 ivar filtervariants: Filter variants across replicates or multiple samples aligned using the same reference ivar consensus 1.4.3+galaxy0 ivar consensus: Call consensus from aligned BAM file ivar getmasked 1.2.2+galaxy0 ivar getmasked: Detect primer mismatches and get primer indices for the amplicon to be masked ivar removereads 1.4.3+galaxy0 ivar removereads: Remove reads from trimmed BAM file
IWTomics	Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.		iwtomics	Statistics and probability	IWTomics: Testing high-resolution sequence-based 'Omics' data at multiple locations and scales		GPL-2.0		3 tools Tool Name Description IWTomics Load 1.0.0.0 IWTomics Load: Smooth and Plot IWTomics Plot with Threshold 1.0.0.0 IWTomics Plot with Threshold: on Test Scale IWTomics Test 1.0.0.0 IWTomics Test: and Plot
jags	JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.		jags	Statistics and probability			GPL-2.0						4.3.0-foss-2021a
jasminesv	JASMINE (Jointly Accurate Sv Merging with Intersample Network Edges) is an automated pipeline for alignment and SV calling in long-read datasets. The tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine represents the set of all SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples.		jasminesv	Structural variation DNA polymorphism Workflows Mapping RNA-Seq	10.1101/2021.05.27.445886		MIT				1.1.4
Java Development Kit (JDK)			jdk								11.0.2
jbigkit			jbigkit										2.1-gcccore-10.3.02.1-gcccore-11.3.0 (D) 2.1-gcccore-10.3.02.1-gcccore-11.3.0 (D)
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.		jbrowse	Genomics	10.1101/gr.094607.109	JBrowse			2 tools Tool Name Description JBrowse 1.16.11+galaxy1 JBrowse: genome browser JBrowse - Data Directory to Standalone 1.16.11+galaxy1 JBrowse - Data Directory to Standalone: upgrades the bare data directory to a full JBrowse instance
JCVI			jcvi						Genome annotation statistics 0.8.4
jellyfish	A command-line algorithm for counting k-mers in DNA sequence.		jellyfish	Sequence analysis Genomics	10.1093/bioinformatics/btr011	jellyfish	GPL-3.0		jellyfish 2.3.0+galaxy1	2.3.0			2.3.0-gcc-10.3.02.3.0-gcc-11.3.0 (D) 2.3.0-gcc-10.3.02.3.0-gcc-11.3.0 (D)
jq			jq						JQ 1.0
Juicer	Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps.		juicer	Sequencing Mapping Genomics Epigenetics	Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments		MIT						1.6
jupyterlab			jupyterlab							3.4.3-py3.9			3.5.0-gcccore-11.3.0
Kallisto	A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.		kallisto	Transcriptomics RNA-seq Gene expression	Near-optimal probabilistic RNA-seq quantification		BSD-2-Clause		2 tools Tool Name Description Kallisto pseudo 0.48.0+galaxy1 Kallisto pseudo: run pseudoalignment on RNA-Seq transcripts Kallisto quant 0.48.0+galaxy1 Kallisto quant: quantify abundances of RNA-Seq transcripts				0.48.0-gompi-2021a0.48.0-gompi-2022a0.48.0--h15996b6_2 0.48.0-gompi-2021a0.48.0-gompi-2022a0.48.0--h15996b6_2 0.48.0-gompi-2021a0.48.0-gompi-2022a0.48.0--h15996b6_2
KAT	Suite of tools that generate, analyse and compare k-mer spectra produced from sequence files		kat	Sequence analysis Genomics	KAT: A K-mer analysis toolkit to quality control NGS datasets and genome assemblies		GPL-3.0				2.4.2
kentutils			kentutils								0.0
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.		khmer	Sequence assembly	4 publications Publications The khmer software package: Enabling efficient nucleotide sequence analysis Scaling metagenome sequence assembly with probabilistic de Bruijn graphs These are not the K-mers you are looking for: Efficient online K-mer counting using a probabilistic data structure 10.7287/peerj.preprints.890v1	khmer	BSD-3-Clause		8 tools Tool Name Description khmer: Abundance Distribution 3.0.0a3+galaxy2 khmer: Abundance Distribution: Calculate abundance distribution of k-mers using pre-made k-mer countgraphs khmer: Abundance Distribution (all-in-one) 3.0.0a3+galaxy2 khmer: Abundance Distribution (all-in-one): Calculate abundance distribution of k-mers khmer: Count Median 3.0.0a3+galaxy2 khmer: Count Median: Count the median/avg k-mer abundance for each sequence khmer: Extract partitions 3.0.0a3+galaxy2 khmer: Extract partitions: Separate sequences that are annotated with partitions into grouped files khmer: Filter reads 3.0.0a3+galaxy2 khmer: Filter reads: by minimal k-mer abundance khmer: Filter reads 3.0.0a3+galaxy2 khmer: Filter reads: below k-mer abundance of 50 khmer: Normalize By Median 3.0.0a3+galaxy2 khmer: Normalize By Median: Filter reads using digital normalization via k-mer abundances khmer: Sequence partition all-in-one 3.0.0a3+galaxy2 khmer: Sequence partition all-in-one: Load, partition, and annotate sequences
KMC	KMC is a utility designed for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects.		kmc	Whole genome sequencing Genomics Sequence assembly	KMC 2: Fast and resource-frugal k-mer counting	KMC					3.2.13.2.4 3.2.13.2.4
kofamscan	KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.		kofamscan	Genomics			MIT						1.3.0--hdfd78af_2
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.		kraken	Taxonomy Metagenomics	Kraken: Ultrafast metagenomic sequence classification using exact alignments	kraken	GFDL-1.3		9 tools Tool Name Description Convert Kraken 1.2+galaxy0 Convert Kraken: data to Galaxy taxonomy representation Kraken 1.3.1 Kraken: assign taxonomic labels to sequencing reads Kraken-filter 1.3.1 Kraken-filter: filter classification by confidence score Kraken-report 1.3.1 Kraken-report: view sample report of a classification Kraken-mpa-report 1.2.4 Kraken-mpa-report: view report of classification for multiple samples Kraken-translate 1.3.1 Kraken-translate: convert taxonomy IDs to names Krakentools: Convert kraken report file 1.2+galaxy1 Krakentools: Convert kraken report file: to krona text file Kraken-biom 1.2.0+galaxy1 Kraken-biom: Create BIOM-format tables from kraken output Krakentools: Extract Kraken Reads By ID 1.2+galaxy1 Krakentools: Extract Kraken Reads By ID: Extract reads that were classified by the Kraken family at specified taxonomic IDs
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.		kraken2	Taxonomy Metagenomics	10.1101/762302		MIT		Kraken2 2.1.3+galaxy1				2.1.2-gompi-2021a2.1.2-gompi-2022a (D) 2.1.2-gompi-2021a2.1.2-gompi-2022a (D)
krakentools	KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files		krakentools	Taxonomy Metagenomics		krakentools	GPL-3.0		4 tools Tool Name Description Krakentools: Combine multiple Kraken reports 1.2+galaxy2 Krakentools: Combine multiple Kraken reports: into a combined report file Krakentools: calculates beta diversity (Bray-Curtis dissimilarity) 1.2+galaxy1 Krakentools: calculates beta diversity (Bray-Curtis dissimilarity): from Kraken, Krona and Bracken files Krakentools: Calculates alpha diversity 1.2+galaxy1 Krakentools: Calculates alpha diversity: from the Bracken abundance estimation file Krakentools: Convert kraken report file 1.2+galaxy1 Krakentools: Convert kraken report file: to MetaPhlAn-style
krona	Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome).		krona	Metagenomics	Interactive metagenomic visualization in a Web browser	krona	Proprietary		2 tools Tool Name Description Krona pie chart 2.7.1+galaxy0 Krona pie chart: from taxonomic profile Visualize with Krona 1 Visualize with Krona: Visualise any hierarchical data
kronatools			kronatools										2.8.1-gcccore-11.3.0
LAMA (Lightweight Analysis of Morphological Abnormalities)	Automated image analysis for developmental phenotyping of mouse embryos. LAMA (Lightweight Analysis of Morphological Abnormalities). Welcome to LAMA, an open source pipeline to automatically identify embryo dysmorphology from 3D volumetric images.		lama	Tomography Genotype and phenotype MRI Workflows	10.1101/2020.05.04.075853						0.9.1001.0.01.0.11.0.2 0.9.1001.0.01.0.11.0.2 0.9.1001.0.01.0.11.0.2 0.9.1001.0.01.0.11.0.2
lastz	A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically.		lastz	Genomics					3 tools Tool Name Description LASTZ_D 1.04.22+galaxy0 LASTZ_D: : estimate substitution scores matrix LASTZ 1.04.22+galaxy0 LASTZ: : align long sequences Lastz paired reads 1.1.1 Lastz paired reads: map short paired reads against reference sequence		1.04.15
length_and_gc_content			length_and_gc_content						Gene length and GC content 0.1.2
LFQ-Analyst	An Easy-To-Use Interactive Web Platform To Analyze and Visualize Label-Free Proteomics Data Preprocessed with MaxQuant. A tool for analysing label-free quantitative proteomics dataset https://bioinformatics.erc.monash.edu/apps/LFQ-Analyst/. LFQ-Analyst: An easy-to-use interactive web-platform to analyze and visualize proteomics data preprocessed with MaxQuant. LFQ-Analyst is an easy-to-use, interactive web application developed to perform differential expression analysis with “one click” and to visualize label-free quantitative proteomic datasets preprocessed with MaxQuant. LFQ-Analyst provides a wealth of user-analytic features and offers numerous publication-quality result output graphics and tables to facilitate statistical and exploratory analysis of label-free quantitative datasets		LFQ-Analyst	Proteomics Sequence analysis Small molecules Metabolomics Proteomics experiment	Lfq-Analyst: An easy-To-use interactive web platform to analyze and visualize label-free proteomics data preprocessed with maxquant		GPL-3.0		LFQ Analyst 1.2.6+galaxy0
liftOver1			liftOver1						Convert genome coordinates 1.0.6
limma	Data analysis, linear models and differential expression for microarray data.		limma	Molecular biology Genetics	Limma powers differential expression analyses for RNA-sequencing and microarray studies	limma	GPL-2.0		limma 3.58.1+galaxy0
LINKS	LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS.		links	Sequence assembly Mapping Sequencing	LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads		GPL-3.0		LINKS 2.0.1+galaxy+1
lofreq	LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.		lofreq	Genomics Genetic variation	LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets		MIT		5 tools Tool Name Description Add LoFreq alignment quality scores 2.1.5+galaxy1 Add LoFreq alignment quality scores: to aligned read SAM/BAM records Call variants 2.1.5+galaxy2 Call variants: with LoFreq Lofreq filter 2.1.5+galaxy0 Lofreq filter: called variants posteriorly Insert indel qualities 2.1.5+galaxy1 Insert indel qualities: into a BAM file Realign reads 2.1.5+galaxy0 Realign reads: with LoFreq viterbi
longshot	Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs a phased VCF file with variants and haplotype information. It can also genotype and phase input VCF files. It can output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs), but it can genotype indels if they are given in an input VCF.		longshot	Genetic variation	Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing		MIT				0.4.1
lpsolve			lpsolve								5.5.2.11		5.5.2.11-gcc-10.3.05.5.2.11-gcc-11.3.0 (D) 5.5.2.11-gcc-10.3.05.5.2.11-gcc-11.3.0 (D)
LTR_retriever	LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.		ltr_retriever	Sequence assembly	LTR_retriever: A highly accurate and sensitive program for identification of long terminal repeat retrotransposons		GPL-3.0				2.9.4
Lua			lua										5.4.3-gcccore-10.3.05.4.4-gcccore-11.3.0 (D) 5.4.3-gcccore-10.3.05.4.4-gcccore-11.3.0 (D)
macs2	Model-based Analysis of ChIP-seq data.		macs2	ChIP-seq Molecular interactions, pathways and networks Transcription factors and regulatory sites	Model-based analysis of ChIP-Seq (MACS)		Artistic-2.0		10 tools Tool Name Description MACS2 bdgdiff 2.2.9.1+galaxy0 MACS2 bdgdiff: Differential peak detection based on paired four bedgraph files MACS2 refinepeak 2.2.9.1+galaxy0 MACS2 refinepeak: Refine peak summits and give scores measuring balance of forward- backward tags (Experimental) MACS2 randsample 2.2.9.1+galaxy0 MACS2 randsample: Randomly sample number or percentage of total reads MACS2 bdgbroadcall 2.2.9.1+galaxy0 MACS2 bdgbroadcall: Call broad peaks from bedGraph output MACS2 filterdup 2.2.9.1+galaxy0 MACS2 filterdup: Remove duplicate reads at the same position MACS2 bdgpeakcall 2.2.9.1+galaxy0 MACS2 bdgpeakcall: Call peaks from bedGraph output MACS2 callpeak 2.2.9.1+galaxy0 MACS2 callpeak: Call peaks from alignment results MACS2 bdgcmp 2.2.9.1+galaxy0 MACS2 bdgcmp: Deduct noise by comparing two signal tracks in bedGraph MACS2 predictd 2.2.9.1+galaxy0 MACS2 predictd: Predict 'd' or fragment size from alignment results MACS2.1.2 2.1.2.0 MACS2.1.2: Model-based Analysis of ChIP-Seq: peak calling				2.2.9.1
maeparser			maeparser										1.3.0-gompi-2021a1.3.0-gompi-2022a (D) 1.3.0-gompi-2021a1.3.0-gompi-2022a (D)
mafft	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.		mafft	Sequence analysis	6 publications Publications MAFFT: Iterative refinement and additional methods 10.7490/f1000research.1114334.1 Parallelization of MAFFT for large-scale multiple sequence alignments MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization MAFFT multiple sequence alignment software version 7: Improvements in performance and usability MAFFT version 5: Improvement in accuracy of multiple sequence alignment		BSD-Source-Code		2 tools Tool Name Description MAFFT 7.526+galaxy0 MAFFT: Multiple alignment program for amino acid or nucleotide sequences MAFFT add 7.526+galaxy0 MAFFT add: Align a sequence,alignment or fragments to an existing alignment.		7.5057.525 7.5057.525		7.490-gcc-10.3.0-with-extensions
MAGeCK	Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology.		MAGeCK	Genetics Genetic variation Genomics	Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR				5 tools Tool Name Description MAGeCK count 0.5.9.2.4 MAGeCK count: - collect sgRNA read counts from read mapping files MAGeCK GSEA 0.5.9.2 MAGeCK GSEA: - a fast implementation of Gene Set Enrichment Analysis MAGeCK mle 0.5.9.2.1 MAGeCK mle: - perform maximum-likelihood estimation of gene essentiality scores MAGeCK pathway 0.5.9.2 MAGeCK pathway: - given a ranked gene list, test whether one pathway is enriched MAGeCKs test 0.5.9.2.1 MAGeCKs test: - given a table of read counts, perform the sgRNA and gene ranking
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.		maker	Genomics DNA Sequence analysis	2 publications Publications 10.1101/gr.6743907 10.1186/1471-2105-12-491	MAKER	Artistic-2.0		2 tools Tool Name Description Maker 2.31.11+galaxy2 Maker: genome annotation pipeline Map annotation ids 2.31.11 Map annotation ids: on a Maker annotation		3.01.04	3.01.03--pl526hb8757ab_0	3.01.03--pl5262h8f1cd36_2
MALDIquant	MALDIquant is a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.		maldi_quant	Proteomics experiment Proteomics	Maldiquant: A versatile R package for the analysis of mass spectrometry data		GPL-3.0		2 tools Tool Name Description MALDIquant peak detection 1.22.0.0 MALDIquant peak detection: Peak detection, binning and filtering for mass-spectrometry imaging data MALDIquant preprocessing 1.22.0.0 MALDIquant preprocessing: Preprocessing of mass-spectrometry imaging data
Manipulate Expression Set Object			music_manipulate_eset						Manipulate Expression Set Object 0.1.1+galaxy4
mash	Fast genome and metagenome distance estimation using MinHash.		mash	Genomics Metagenomics Statistics and probability Sequence analysis DNA mutation	10.1186/s13059-016-0997-x	mash	CC-BY-4.0		2 tools Tool Name Description mash screen 2.3+galaxy3 mash screen: determines how well query sequences are contained within a pool of sequences mash sketch 2.3+galaxy0 mash sketch: Create a reduced representation of a sequence or set of sequences, based on min-hashes				2.3-gcc-10.3.0
master2pgSnp			master2pgSnp						MasterVar to pgSnp 1.0.0
MaSuRCA	Whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454).		masurca	Sequence assembly Whole genome sequencing Sequence analysis	The MaSuRCA genome assembler				MaSuRCA simple 4.0.6+galaxy0
Matchms	Tool to import, process, clean, and compare mass spectrometry data.		matchms	Metabolomics			Apache-2.0		11 tools Tool Name Description recetox-xMSannotator 0.10.0+galaxy1 recetox-xMSannotator: annotate peak intensity table including scores and confidence levels matchms split library 0.27.0+galaxy0 matchms split library: split a large library into subsets matchms networking 0.27.0+galaxy0 matchms networking: create similarity network graph from matchms similarity scores matchms metadata export 0.27.0+galaxy0 matchms metadata export: extract all metadata from mass spectra file to tabular format matchms fingerprint similarity 0.27.0+galaxy0 matchms fingerprint similarity: calculate similarity between molecular fingerprints calculated from structural spectrum metadata descriptors matchms filtering 0.27.0+galaxy0 matchms filtering: filter and normalize mass spectrometry data matchms convert 0.27.0+galaxy0 matchms convert: convert between mass spectral library formats (.mgf/.msp/.json) using matchms matchms scores formatter 0.27.0+galaxy0 matchms scores formatter: reformat scores object of matchms to long format table matchms metadata match 0.27.0+galaxy0 matchms metadata match: matchms metadata match calculation for numeric fields based on tolerance matchms similarity 0.20.0+galaxy0 matchms similarity: calculate the similarity score and matched peaks matchms spectral similarity 0.27.0+galaxy0 matchms spectral similarity: matchms spectral similarity calculation
matplotlib	Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python. Matplotlib makes easy things easy and hard things possible.		matplotlib				MIT						3.4.2-foss-2021a3.5.2-foss-2022a (D) 3.4.2-foss-2021a3.5.2-foss-2022a (D)
MaxBin2	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.		maxbin	Metagenomics Sequence assembly Microbiology	26515820				MaxBin2 2.2.7+galaxy2
MaxQuant	Quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.		maxquant	Proteomics experiment Proteomics Statistics and probability	4 publications Publications Visualization of LC-MS/MS proteomics data in MaxQuant MaxQuant for in-depth analysis of large SILAC datasets MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification MaxQuant.Live Enables Enhanced Selectivity and Identification of Peptides Modified by Endogenous SUMO and Ubiquitin	MaxQuant			3 tools Tool Name Description MaxQuant (using mqpar.xml) 2.0.3.0+galaxy0 MaxQuant (using mqpar.xml): MaxQuant 2.0.3.0+galaxy0 MaxQuant: MaxQuant (using mqpar.xml) 1.6.10.43 MaxQuant (using mqpar.xml):				2.2.0.0-gcccore-11.3.0
mcl	MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields.		mcl	Molecular interactions, pathways and networks	10.1007/978-1-61779-361-5_15	mcl	GPL-3.0				14-137
MCQUANT			mcquant						MCQUANT 1.5.3+galaxy1
mdanalysis	MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, Amber or DL_POLY; it also reads other formats (e.g. PDB files and XYZ format trajectories; see the supported coordinate formats for the full list). It can write most of these formats, too, together with atom selections for use in Gromacs, CHARMM, VMD and PyMol		mdanalysis	Molecular dynamics	MDAnalysis: A toolkit for the analysis of molecular dynamics simulations		GPL-2.0		Cosine Content 1.0.0+galaxy0
MDTraj			MDTraj						2 tools Tool Name Description Slice MD trajectories 1.9.7+galaxy0 Slice MD trajectories: using the MDTraj package MDTraj file converter 1.9.6+galaxy0 MDTraj file converter: - interconvert between MD trajectory file formats.
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.		medaka	Sequence assembly Machine learning			MPL-2.0		4 tools Tool Name Description medaka variant pipeline 1.4.4+galaxy1 medaka variant pipeline: via neural networks medaka consensus tool 1.7.2+galaxy0 medaka consensus tool: Assembly polishing via neural networks medaka consensus pipeline 1.7.2+galaxy1 medaka consensus pipeline: Assembly polishing via neural networks medaka variant tool 1.7.2+galaxy1 medaka variant tool: decodes variant calls from medaka consensus output				1.9.1
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.		megahit	Metagenomics Sequencing Ecology Sequence assembly	MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph				2 tools Tool Name Description megahit contig2fastg 1.1.3+galaxy1 megahit contig2fastg: for converting MEGAHIT's contigs (.fa) to assembly graphs (.fastg) MEGAHIT 1.2.9+galaxy1 MEGAHIT: for metagenomics assembly				1.2.9-gcccore-10.3.01.2.9-gcccore-11.3.0 (D) 1.2.9-gcccore-10.3.01.2.9-gcccore-11.3.0 (D)
Merge Columns			merge_cols						Merge Columns 1.0.3
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.		merqury	Sequence assembly Whole genome sequencing Plant biology	10.1101/2020.03.15.992941				2 tools Tool Name Description Merqury 1.3+galaxy4 Merqury: evaluate the assembly quality Merqury histogram plot 1.3+galaxy4 Merqury histogram plot: evaluate the assembly quality		1.3
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.		meryl	Whole genome sequencing Genomics Sequence analysis Sequencing	10.1186/s13059-020-02134-9		Freeware		Meryl 1.3+galaxy6		1.4.1
metabat	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		metabat	Metagenomics Sequence assembly Metagenomic sequencing	2 publications Publications MetaBAT 2: An adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities				MetaBAT2 2.15+galaxy3
MetaDEGalaxy	Galaxy workflow for differential abundance analysis of 16s metagenomic data. You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota. This history is empty. You can load your own data or get data from an external source		MetaDEGalaxy	Metagenomics Metagenomic sequencing Workflows Microbial ecology RNA-Seq	MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data				9 tools Tool Name Description PEAR Statistics 1.0.0 PEAR Statistics: Generate paired-end reads overlap Statistic from PEAR log file Phyloseq Abundance plot 1.22.3.3 Phyloseq Abundance plot: Phyloseq Abundance Plot with the factors of choice Phyloseq Abundance Taxonomy 1.22.3.3 Phyloseq Abundance Taxonomy: Phyloseq Abundance Plot on Taxonomy level Phyloseq DESeq2 1.22.3 Phyloseq DESeq2: Perform differential expression analysis of BIOM file Phyloseq Network Plot 1.24.2 Phyloseq Network Plot: Phyloseq Network Plot Phyloseq Richness 1.22.3.2 Phyloseq Richness: Phyloseq Richness Plot reheader 1.0.0 reheader: Rename sequence header in FASTQ file Symmetric Plot 1.0.1 Symmetric Plot: Symmetric Plot OTUTable 1.0.0 OTUTable: Convert UCLUST format from Vsearch to OTU Table
metaeuk	MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics		metaeuk	Metagenomics Gene and protein families	2 publications Publications 10.1186/s40168-020-00808-x 10.1101/851964		GPL-3.0				5-34c21f2		5-gcc-10.3.06-gcc-11.3.0 (D) 5-gcc-10.3.06-gcc-11.3.0 (D)
MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.		metaphlan	Metagenomics Phylogenomics	Metagenomic microbial community profiling using unique clade-specific marker genes		MIT		4 tools Tool Name Description MetaPhlAn 4.1.1+galaxy1 MetaPhlAn: to profile the composition of microbial communities Merge 4.1.1+galaxy0 Merge: MetaPhlAn abundance tables MetaPhlAn2 2.6.0.1 MetaPhlAn2: to profile the composition of microbial communities Format MetaPhlAn2 2.6.0.0 Format MetaPhlAn2: output for Krona
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.		metaQuantome	Proteomics Metatranscriptomics Microbial ecology Proteomics experiment Metagenomics	2 publications Publications MetaQuantome: An integrated, quantitative metaproteomics approach reveals connections between taxonomy and protein function in complex microbiomes Updates on metaQuantome Software for Quantitative Metaproteomics				6 tools Tool Name Description metaQuantome: database 2.0.2+galaxy0 metaQuantome: database: download the GO, EC, and NCBI databases metaQuantome: expand 2.0.2+galaxy0 metaQuantome: expand: a set of functional or taxonomy annotations metaQuantome: filter 2.0.2+galaxy0 metaQuantome: filter: for quality, redundancy, and sample coverage metaQuantome: create samples file 2.0.2+galaxy0 metaQuantome: create samples file: by specifying the experiment's groups and associated column names metaQuantome: stat 2.0.2+galaxy0 metaQuantome: stat: differential analysis of functional expression and taxonomic abundance metaQuantome: visualize 2.0.2+galaxy0 metaQuantome: visualize: taxonomic analysis, functional analysis, and function-taxonomy analysis results
metaspades	Genome assembler for metagenomics datasets.		metaspades	Metagenomics Sequence analysis	3 publications Publications SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update 10.7490/f1000research.1114334.1				metaSPAdes 3.15.5+galaxy2
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.		metawrap	Whole genome sequencing Metagenomic sequencing Metagenomics	MetaWRAP - A flexible pipeline for genome-resolved metagenomic data analysis 08 Information and Computing Sciences 0803 Computer Software 08 Information and Computing Sciences 0806 Information Systems		MIT		MetaWRAP 1.3.0+galaxy1
MethylDackel	A (mostly) universal methylation extractor for BS-seq experiments.		MethylDackel	Epigenomics			MIT		MethylDackel 0.5.2+galaxy0
metilene			metilene						metilene 0.2.6.1
MIGRATE	Estimates effective population sizes,past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes, and population divergences or admixture.		MIGRATE	Population genetics Nucleic acid structure analysis Zoology	2 publications Publications Unified framework to evaluate panmixia and migration direction among multiple sampling locations Fractional coalescent		MIT
Mikado	A lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data and to select the best models in each locus.		mikado	RNA-seq Gene transcripts	Leveraging multiple transcriptome assembly methods for improved gene structure annotation		LGPL-3.0						2.2.4--py39h70b41aa_0
MiModD			mimodd						14 tools Tool Name Description MiModD Read Alignment 0.1.9 MiModD Read Alignment: maps sequence reads to a reference genome using SNAP MiModD Variant Calling 0.1.9 MiModD Variant Calling: generates a BCF file of position-specific variant likelihoods and coverage information based on a reference sequence and reads aligned against it MiModD Coverage Statistics 0.1.9 MiModD Coverage Statistics: calculates coverage statistics for a BCF file as generated by the MiModd Variant Calling tool MiModD Run Annotation 0.1.9 MiModD Run Annotation: writes run metadata in SAM format for attaching it to sequenced reads data MiModD File Information 0.1.9 MiModD File Information: provides summary reports for supported sequence data formats. MiModD Reheader 0.1.9 MiModD Reheader: takes a BAM file and generates a copy with the original header (if any) replaced or modified by that found in a template SAM file MiModD NacreousMap 0.1.9 MiModD NacreousMap: maps phenotypically selected variants by multi-variant linkage analysis MiModD Report Variants 0.1.9 MiModD Report Variants: in a human-friendly format that simplifies data exploration MiModD Deletion Calling (for PE data) 0.1.9 MiModD Deletion Calling (for PE data): predicts deletions in one or more aligned paired-end read samples based on coverage of the reference genome and on insert sizes MiModD Extract Variant Sites 0.1.9 MiModD Extract Variant Sites: from a BCF file MiModD Rebase Sites 0.1.9 MiModD Rebase Sites: from a VCF file MiModD Convert 0.1.9 MiModD Convert: converts sequence data into different formats MiModD Sort 0.1.9 MiModD Sort: takes a SAM/BAM dataset and generates a coordinate/name-sorted copy MiModD VCF Filter 0.1.9 MiModD VCF Filter: extracts lines from a vcf variant file based on field-specific filters
minia	Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.		minia	Sequence assembly	Using cascading Bloom filters to improve the memory usage for de Brujin graphs	minia	CECILL-2.0		Minia 3.2.6
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.		miniasm	Genomics Sequence assembly	Minimap and miniasm: Fast mapping and de novo assembly for noisy long sequences		MIT		miniasm 0.3_r179+galaxy1		0.3
miniconda			miniconda								4.12.0		4.12.0
minigraph			minigraph								0.20
minimap2	Pairwise aligner for genomic and spliced nucleotide sequences		minimap2	Mapping	Minimap2: Pairwise alignment for nucleotide sequences	minimap2	MIT		Map with minimap2 2.28+galaxy0	2.17 2.22 2.24	2.26		2.24-gcccore-11.3.0
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.		miniprot	Sequence sites, features and motifs Sequence analysis			MIT				0.5
mira	MIRA 3 - Whole Genome Shotgun and EST Sequence Assembler		mira	Sequence assembly RNA-Seq	Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs	mira	GPL-3.0						4.9.6--1
miRcounts			mircounts						miRcounts 1.4.0
mirdeep2	miRDeep2 discovers active known or novel miRNAs from deep sequencing data.		mirdeep2	Functional, regulatory and non-coding RNA RNA immunoprecipitation			GPL-3.0		3 tools Tool Name Description MiRDeep2 2.0.1.2+galaxy0 MiRDeep2: identification of novel and known miRNAs MiRDeep2 Mapper 2.0.0.8.1 MiRDeep2 Mapper: process and map reads to a reference genome MiRDeep2 Quantifier 2.0.0 MiRDeep2 Quantifier: fast quantitation of reads mapping to known miRBase precursors
MITObim			mitobim						MITObim 1.9.1
MitoHiFi	Find, circularise and annotate mitogenome from PacBio assemblies		mitohifi	Sequence assembly Sequence analysis Genomics	MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics		MIT		MitoHiFi 3+galaxy0
mitos	De novo metazoan mitochondrial genome annotation.		mitos2	Zoology Whole genome sequencing	10.1016/j.ympev.2012.08.023				MITOS2 2.1.9+galaxy0
MLST	Multi Locus Sequence Typing from an assembled genome or from a set of reads.		mlst	Immunoproteins and antigens	Multilocus sequence typing of total-genome-sequenced bacteria	MLST	Other		2 tools Tool Name Description MLST 2.22.0 MLST: Scans genomes against PubMLST schemes MLST List 2.22.0 MLST List: Lists available schemes for the MLST tool				2.23.0--hdfd78af_1
MMseqs2	MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed. MMseqs2 includes Linclust, the first clustering algorithm whose runtime scales linearly With Linclust we clustered 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity.		mmseqs2	Metagenomics Sequence analysis Proteins Nucleic acids Gene and protein families Taxonomy	6 publications Publications MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets 10.1101/079681 Clustering huge protein sequence sets in linear time MMseqs2 desktop and local web server app for fast, interactive sequence searches 10.1101/2020.11.27.401018 10.1093/bioinformatics/btab184		GPL-3.0				13-45111
MOB-suite	Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance. MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Plasmids are mobile genetic elements (MGEs), which allow for rapid evolution and adaption of bacteria to new niches through horizontal transmission of novel traits to different genetic backgrounds. The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies.		mob-suite	Mobile genetic elements Whole genome sequencing Public health and epidemiology Sequence assembly Biomarkers	Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance				2 tools Tool Name Description MOB-Recon 3.0.3+galaxy0 MOB-Recon: Type contigs and extract plasmid sequences MOB-Typer 3.0.3+galaxy0 MOB-Typer: Get the plasmid type and mobility given its sequence
moFF	A modest Feature Finder to extract features in MS1 Data.		moff	Proteomics	MoFF: A robust and automated approach to extract peptide ion intensities				moFF 2.0.3.0
MONAI Label			monailabel								0.6.00.7.00.8.0 0.6.00.7.00.8.0 0.6.00.7.00.8.0
Morpheus	A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.		morpheus	Proteomics	A proteomics search algorithm specifically designed for high-resolution tandem mass spectra		MIT		Morpheus 288+galaxy0
mosdepth	Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.		mosdepth	Statistics and probability Data quality management	Mosdepth: Quick coverage calculation for genomes and exomes	mosdepth	MIT		mosdepth 0.3.8+galaxy0
Mothur	Open-source, platform-independent, community-supported software for describing and comparing microbial communities		mothur	Microbial ecology Taxonomy Sequence analysis Phylogeny	10.1128/AEM.01541-09		GPL-3.0		131 tools Tool Name Description Align.check 1.39.5.0 Align.check: Calculate the number of potentially misaligned bases Align.seqs 1.39.5.0 Align.seqs: Align sequences to a template alignment Amova 1.39.5.0 Amova: Analysis of molecular variance Anosim 1.39.5.0 Anosim: Non-parametric multivariate analysis of changes in community structure Bin.seqs 1.39.5.0 Bin.seqs: Order Sequences by OTU Biom.info 1.39.5.0 Biom.info: create shared and taxonomy files from biom Chimera.bellerophon 1.39.5.0 Chimera.bellerophon: Find putative chimeras using bellerophon Chimera.ccode 1.39.5.0 Chimera.ccode: Find putative chimeras using ccode Chimera.check 1.39.5.0 Chimera.check: Find putative chimeras using chimeraCheck Chimera.perseus 1.39.5.0 Chimera.perseus: Find putative chimeras using chimeraCheck Chimera.pintail 1.39.5.0 Chimera.pintail: Find putative chimeras using pintail Chimera.slayer 1.39.5.0 Chimera.slayer: Find putative chimeras using slayer Chimera.uchime 1.39.5.0 Chimera.uchime: Find putative chimeras using uchime Chimera.vsearch 1.39.5.2 Chimera.vsearch: find potential chimeric sequences using vsearch Chop.seqs 1.39.5.0 Chop.seqs: Trim sequences to a specified length Classify.otu 1.39.5.0 Classify.otu: Assign sequences to taxonomy Classify.rf 1.36.1.0 Classify.rf: description Classify.seqs 1.39.5.0 Classify.seqs: Assign sequences to taxonomy Classify.tree 1.39.5.0 Classify.tree: Get a consensus taxonomy for each node on a tree Clearcut 1.39.5.0 Clearcut: Generate a tree using relaxed neighbor joining Cluster 1.39.5.0 Cluster: Assign sequences to OTUs (Operational Taxonomic Unit) Cluster.classic 1.39.5.0 Cluster.classic: Assign sequences to OTUs (Dotur implementation) Cluster.fragments 1.39.5.0 Cluster.fragments: Group sequences that are part of a larger sequence Cluster.split 1.39.5.0 Cluster.split: Assign sequences to OTUs and split large matrices Collect.shared 1.39.5.0 Collect.shared: Generate collector's curves for calculators on OTUs Collect.single 1.39.5.0 Collect.single: Generate collector's curves for OTUs Consensus.seqs 1.39.5.0 Consensus.seqs: Find a consensus sequence for each OTU or phylotype Cooccurrence 1.39.5.0 Cooccurrence: tests whether presence-absence patterns differ from chance Corr.axes 1.39.5.0 Corr.axes: correlation of data to axes Count.groups 1.39.5.0 Count.groups: counts the number of sequences represented by a specific group or set of groups Count.seqs 1.39.5.0 Count.seqs: (aka make.table) counts the number of sequences represented by the representative Create.database 1.39.5.0 Create.database: creates a database file from a list, repnames, repfasta and contaxonomy file Degap.seqs 1.39.5.0 Degap.seqs: Remove gap characters from sequences Deunique.seqs 1.39.5.0 Deunique.seqs: Return all sequences Deunique.tree 1.39.5.0 Deunique.tree: Reinsert the redundant sequence identiers back into a unique tree. Dist.seqs 1.39.5.0 Dist.seqs: calculate uncorrected pairwise distances between aligned sequences Dist.shared 1.39.5.0 Dist.shared: Generate a phylip-formatted dissimilarity distance matrix among multiple groups Fastq.info 1.39.5.0 Fastq.info: Convert fastq to fasta and quality Filter.seqs 1.39.5.0 Filter.seqs: removes columns from alignments Filter.shared 1.39.5.0 Filter.shared: remove OTUs based on various critieria Get.communitytype 1.39.5.0 Get.communitytype: description Get.coremicrobiome 1.39.5.0 Get.coremicrobiome: fraction of OTUs for samples or abundances Get.dists 1.39.5.0 Get.dists: selects distances from a phylip or column file Get.group 1.39.5.0 Get.group: group names from shared or from list and group Get.groups 1.39.5.0 Get.groups: Select groups Get.label 1.39.5.0 Get.label: label names from list, sabund, or rabund file Get.lineage 1.39.5.0 Get.lineage: Picks by taxon Get.mimarkspackage 1.39.5.0 Get.mimarkspackage: creates a mimarks package form with your groups Get.otulabels 1.39.5.0 Get.otulabels: Selects OTU labels Get.otulist 1.39.5.0 Get.otulist: Get otus for each distance in a otu list Get.oturep 1.39.5.0 Get.oturep: Generate a fasta with a representative sequence for each OTU Get.otus 1.39.5.0 Get.otus: Get otus containing sequences from specified groups Get.rabund 1.39.5.0 Get.rabund: Get rabund from a otu list or sabund Get.relabund 1.39.5.0 Get.relabund: Calculate the relative abundance of each otu Get.sabund 1.39.5.0 Get.sabund: Get sabund from a otu list or rabund Get.seqs 1.39.5.0 Get.seqs: Picks sequences by name Get.sharedseqs 1.39.5.0 Get.sharedseqs: Get shared sequences at each distance from list and group Hcluster 1.36.1.0 Hcluster: Assign sequences to OTUs (Operational Taxonomic Unit) Heatmap.bin 1.39.5.0 Heatmap.bin: Generate a heatmap for OTUs Heatmap.sim 1.39.5.0 Heatmap.sim: Generate a heatmap for pariwise similarity Homova 1.39.5.0 Homova: Homogeneity of molecular variance Indicator 1.39.5.0 Indicator: Identify indicator "species" for nodes on a tree Lefse 1.39.5.0 Lefse: description Libshuff 1.39.5.0 Libshuff: Cramer-von Mises tests communities for the same structure List.otulabels 1.39.5.0 List.otulabels: Lists otu labels from shared or relabund file List.seqs 1.39.5.0 List.seqs: Lists the names (accnos) of the sequences Make.biom 1.39.5.0 Make.biom: Make biom files from a shared file Make.contigs 1.39.5.1 Make.contigs: Aligns paired forward and reverse fastq files to contigs as fasta and quality Make Design 1.39.5.0 Make Design: Assign groups to Sets Make.fastq 1.39.5.0 Make.fastq: Convert fasta and quality to fastq Make.group 1.39.5.0 Make.group: Make a group file Make.lefse 1.39.5.0 Make.lefse: create a lefse formatted input file from mothur's output files Make.lookup 1.39.5.0 Make.lookup: allows you to create custom lookup files for use with shhh.flows Make.shared 1.39.5.0 Make.shared: Make a shared file from a list and a group Make.sra 1.39.5.0 Make.sra: creates the necessary files for a NCBI submission Mantel 1.39.5.0 Mantel: Mantel correlation coefficient between two matrices. Merge.count 1.39.5.0 Merge.count: Merge count tables Merge.files 1.39.5.0 Merge.files: Merge data Merge.groups 1.39.5.0 Merge.groups: Merge groups in a shared file Merge.sfffiles 1.39.5.0 Merge.sfffiles: Merge SFF files Merge.taxsummary 1.39.5.0 Merge.taxsummary: Merge tax.summary files Metastats 1.39.5.0 Metastats: generate principle components plot data Mimarks.attributes 1.39.5.0 Mimarks.attributes: Reads bioSample Attributes xml and generates source for get.mimarkspackage command Nmds 1.39.5.0 Nmds: generate non-metric multidimensional scaling data Normalize.shared 1.39.5.0 Normalize.shared: Normalize the number of sequences per group to a specified level Otu.association 1.39.5.0 Otu.association: Calculate the correlation coefficient for the otus Otu.hierarchy 1.39.5.0 Otu.hierarchy: Relate OTUs at different distances Pairwise.seqs 1.39.5.0 Pairwise.seqs: calculate uncorrected pairwise distances between sequences Parse.list 1.39.5.0 Parse.list: Generate a List file for each group Parsimony 1.39.5.0 Parsimony: Describes whether two or more communities have the same structure Pca 1.39.5.0 Pca: Principal Coordinate Analysis for a shared file Pcoa 1.39.5.0 Pcoa: Principal Coordinate Analysis for a distance matrix Pcr.seqs 1.39.5.0 Pcr.seqs: Trim sequences Phylo.diversity 1.39.5.0 Phylo.diversity: Alpha Diversity calculates unique branch length Phylotype 1.39.5.0 Phylotype: Assign sequences to OTUs based on taxonomy Pre.cluster 1.39.5.0 Pre.cluster: Remove sequences due to pyrosequencing errors Primer.design 1.39.5.0 Primer.design: identify sequence fragments that are specific to particular OTUs Rarefaction.shared 1.39.5.0 Rarefaction.shared: Generate inter-sample rarefaction curves for OTUs Rarefaction.single 1.39.5.0 Rarefaction.single: Generate intra-sample rarefaction curves for OTUs Remove.dists 1.39.5.0 Remove.dists: Removes distances from a phylip or column file Remove.groups 1.39.5.0 Remove.groups: Remove groups from groups,fasta,names,list,taxonomy Remove.lineage 1.39.5.0 Remove.lineage: Picks by taxon Remove.otulabels 1.39.5.0 Remove.otulabels: Removes OTU labels Remove.otus 1.39.5.0 Remove.otus: Removes OTUs from various file formats Remove.rare 1.39.5.0 Remove.rare: Remove rare OTUs Remove.seqs 1.39.5.0 Remove.seqs: Remove sequences by name Rename.seqs 1.39.5.0 Rename.seqs: Rename sequences by concatenating the group name Reverse.seqs 1.39.5.0 Reverse.seqs: Reverse complement the sequences Screen.seqs 1.39.5.1 Screen.seqs: Screen sequences Sens.spec 1.39.5.0 Sens.spec: Determine the quality of OTU assignment Seq.error 1.39.5.0 Seq.error: assess error rates in sequencing data Sffinfo 1.39.5.0 Sffinfo: Summarize the quality of sequences Shhh.flows 1.39.5.0 Shhh.flows: Denoise flowgrams (PyroNoise algorithm) Shhh.seqs 1.39.5.0 Shhh.seqs: Denoise program (Quince SeqNoise) Sort.seqs 1.39.5.0 Sort.seqs: put sequences in different files in the same order Split.abund 1.39.5.0 Split.abund: Separate sequences into rare and abundant groups Split.groups 1.39.5.0 Split.groups: Generates a fasta file for each group Sub.sample 1.39.5.0 Sub.sample: Create a sub sample Summary.qual 1.39.5.0 Summary.qual: Summarize the quality scores Summary.seqs 1.39.5.0 Summary.seqs: Summarize the quality of sequences Summary.shared 1.39.5.0 Summary.shared: Summary of calculator values for OTUs Summary.single 1.39.5.2 Summary.single: Summary of calculator values for OTUs Summary.tax 1.39.5.0 Summary.tax: Assign sequences to taxonomy Taxonomy-to-Krona 1.0 Taxonomy-to-Krona: convert a mothur taxonomy file to Krona input format Tree.shared 1.39.5.0 Tree.shared: Generate a newick tree for dissimilarity among groups Trim.flows 1.39.5.0 Trim.flows: partition by barcode, trim to length, cull by length and mismatches Trim.seqs 1.39.5.0 Trim.seqs: Trim sequences - primers, barcodes, quality unifrac.unweighted 1.39.5.0 unifrac.unweighted: Describes whether two or more communities have the same structure unifrac.weighted 1.39.5.0 unifrac.weighted: Describes whether two or more communities have the same structure Unique.seqs 1.39.5.0 Unique.seqs: Return unique sequences Venn 1.39.5.0 Venn: Generate Venn diagrams for groups
mousemine	Data warehouse for accessing mouse data from Mouse Genome Informatics (MGI). Supports powerful query, reporting, and analysis capabilities, the ability to save and combine results from different queries, easy integration into larger workflows, and a comprehensive Web Services layer.		mousemine	Model organisms Genotype and phenotype	MouseMine: a new data warehouse for MGI				MouseMine 1.0.0
MrBayes	Program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. It uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.		mrbayes	Phylogenetics	3 publications Publications MRBAYES: Bayesian inference of phylogenetic trees MrBayes 3: Bayesian phylogenetic inference under mixed models Mrbayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space		GPL-3.0					3.2.7--h19cf415_2	3.2.7a-foss-2022a
MRtrix3	A fast, flexible and open software framework for medical image processing and visualisation | MRtrix3 is an open-source, cross-platform software package for medical image processing, analysis and visualisation, with a particular emphasis on the investigation of the brain using diffusion MRI. It is implemented using a fast, modular and flexible general-purpose code framework for image data access and manipulation, enabling efficient development of new applications, whilst retaining high computational performance and a consistent command-line interface between applications. In this article, we provide a high-level overview of the features of the MRtrix3 framework and general-purpose image processing applications provided with the software		mrtrix	MRI Medical imaging Data visualisation	MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation								3.0.3-foss-2021a
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.		msconvert	Proteomics Proteomics experiment	A cross-platform toolkit for mass spectrometry and proteomics		Apache-2.0		msconvert 3.0.20287.4
MSMetaEnhancer	Tool for mass spectra metadata annotation.		msmetaenhancer	Metabolomics Compound libraries and screening Data submission, annotation and curation	10.21105/joss.04494		MIT		MSMetaEnhancer 0.4.0+galaxy1
MSstats	Statistical tool for quantitative mass spectrometry-based proteomics.		msstats	Proteomics Proteomics experiment Statistics and probability Workflows	MSstats: An R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments	MSstats			MSstats 4.0.0+galaxy1
MSstatsTMT	Tools for detecting differentially abundant peptides and proteins in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling		bioconductor-msstatstmt	Proteomics Proteomics experiment Protein expression					MSstatsTMT 2.0.0+galaxy1
mtag (Multi-Trait Analysis of GWAS)			mtag										20230414
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.		multiqc	Sequencing Bioinformatics Sequence analysis Genomics	10.1093/bioinformatics/btw354	MultiQC	GPL-3.0		MultiQC 1.11+galaxy1	1.9			1.11-foss-2021a1.14-foss-2022a (D) 1.11-foss-2021a1.14-foss-2022a (D)
MUMmer	MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Basically it is a ultra-fast alignment of large-scale DNA and protein sequences		mummer	Genomics Mapping Sequencing	4 publications Publications Alignment of whole genomes MUMmer4: A fast and versatile genome alignment system 10.1186/gb-2004-5-2-r12 Fast algorithms for large-scale genome alignment and comparison	MUMmer	Artistic-2.0		6 tools Tool Name Description Delta-Filter 4.0.0rc1+galaxy3 Delta-Filter: Filters alignment (delta) file from nucmer Show-Coords 4.0.0rc1+galaxy3 Show-Coords: Parse delta file and report coordinates and other information Nucmer 4.0.0rc1+galaxy3 Nucmer: Align two or more sequences Mummerplot 4.0.0rc1+galaxy3 Mummerplot: Generate 2-D dotplot of aligned sequences DNAdiff 4.0.0rc1+galaxy3 DNAdiff: Evaluate similarities/differences between two sequences Mummer 4.0.0rc1+galaxy3 Mummer: Align two or more sequences			3.23--pl5321h1b792b2_13
MuSiC Compare	MuSiC is a suite of programs that evaluate the biophysical effects of amino acid mutations in proteins. They request the experimental or modeled 3-dimensional protein structure as input, and predict the impact of specific single-site mutations requested by the user or of all possible single-site mutations. PoPMuSiC and HoTMuSiC predict the changes in thermodynamic and thermal stability, respectively, upon mutation. They are helpful for the rational design of modified proteins with controlled stability properties. SNPMuSiC predicts whether protein variants are deleterious or benign due to stability issues, thus providing a molecular-level interpretation of disease phenotype.		music_compare	Protein folding, stability and design Genetic variation Computational biology Bioengineering Protein properties	6 publications Publications Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0 PoPMuSiC 2.1: A web server for the estimation of protein stability changes upon mutation and sequence optimality Quantification of biases in predictions of protein stability changes upon mutations Predicting protein thermal stability changes upon point mutations using statistical potentials: Introducing HoTMuSiC Protein Thermal Stability Engineering Using HoTMuSiC Prediction and interpretation of deleterious coding variants in terms of protein structural stability				MuSiC Compare 0.1.1+galaxy4
music_deconvolution			music_deconvolution						3 tools Tool Name Description Construct Expression Set Object 0.1.1+galaxy4 Construct Expression Set Object: Create an ExpressionSet object from tabular and textual data MuSiC Deconvolution 0.1.1+galaxy4 MuSiC Deconvolution: estimate cell type proportions in bulk RNA-seq data Inspect Expression Set Object 0.1.1+galaxy4 Inspect Expression Set Object: Inspect an ExpressionSet object by a variety of attributes
mztosqlite	Convert proteomics data files into a SQLite database		mztosqlite	Proteomics Biological databases					mz to sqlite 2.1.1+galaxy0
nag			nag							nll6i27dbl nll6i27dbl-i8 nll6i27dbl-mkl fll6i26dcl fll6i26dcl-mkl
Naive Variant Caller (NVC)			nvc						Naive Variant Caller (NVC) 0.0.4
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		nanocompore	Functional, regulatory and non-coding RNA RNA-Seq Gene transcripts Transcriptomics Transcription factors and regulatory sites	10.1101/843136		GPL-3.0		SampComp 1.0.0rc3.post2+galaxy1				1.0.4--pyhdfd78af_0
nanofilt			nanofilt						NanoFilt 0.1.0
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		nanoplot	Genomics	NanoPack: Visualizing and processing long-read sequencing data		GPL-3.0		NanoPlot 1.43.0+galaxy0
Nanopolish	A package for detecting cytosine methylations and genetic variations from nanopore MinION sequencing data.		nanopolish	Sequence analysis Sequencing Genetic variation Statistics and probability	Detecting DNA cytosine methylation using nanopore sequencing	Nanopolish	MIT		4 tools Tool Name Description Nanopolish variants 0.14.0+galaxy0 Nanopolish variants: - Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences Nanopolish polyA 0.14.0+galaxy0 Nanopolish polyA: - Estimate the length of the poly-A tail on direct RNA reads. Nanopolish methylation 0.14.0+galaxy0 Nanopolish methylation: - Classify nucleotides as methylated or not. Nanopolish eventalign 0.14.0+galaxy0 Nanopolish eventalign: - Align nanopore events to reference k-mers				0.14.0--hb24e783_1
NanoSV			nanosv								1.2.4
Natural-Product-Likeness Scorer			natural_product_likeness_scorer						Natural Product likeness calculator 2.1
NCBI Datasets	NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface.		ncbi-datasets-cli	Biological databases		NCBI Datasets					14.2.214.13.014.29.116.6.0 14.2.214.13.014.29.116.6.0 14.2.214.13.014.29.116.6.0 14.2.214.13.014.29.116.6.0
NCBI VDB			ncbi-vdb										2.10.9-gompi-2021a3.0.2-gompi-2022a (D) 2.10.9-gompi-2021a3.0.2-gompi-2022a (D)
ncbi_acc_download	The National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site.		ncbi_acc_download	Data integration and warehousing Database management Data mining Molecular interactions, pathways and networks Rare diseases	14 publications Publications Database resources of the National Center for Biotechnology Information. Database resources of the national center for biotechnology information Database resources of the National Center for Biotechnology Information Database resources of the National Center for Biotechnology Information Database resources of the National Center for Biotechnology Information Database resources of the National Center for Biotechnology Information Database resources of the National Center for Biotechnology Information Database resources of the National Center for Biotechnology Information Database resources of the national center for biotechnology information Database resources of the National Center for Biotechnology Information Database resources of the National Center for Biotechnology Information Database resources of the National Center for Biotechnology Information Database resources of the National Center for Biotechnology Information Database Resources of the National Center for Biotechnology Information				NCBI Accession Download 0.2.8+galaxy0
nccmp	nccmp compares two NetCDF files bitwise, semantically or with a user defined tolerance (absolute or relative percentage). Parallel comparisons are done in local memory without requiring temporary files. Highly recommended for regression testing scientific models or datasets in a test-driven development environment.		nccmp				GPL-2.0			1.8.5.0
NCL			ncl							6.6.2
NCO	The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5.		nco				BSD-3-Clause			4.7.7 4.9.2 5.0.5
Ncview	Ncview is a netCDF visual browser.		ncview				GPL-1.0			2.1.7
NetCDF	NetCDF (Network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.		netcdf							4.7.1 4.7.1p 4.6.3 4.6.3p 4.7.3 4.7.3p 4.7.4 4.7.4p 4.6.3-i8r8 4.8.0 4.8.0p 4.9.0 4.9.0p			4.8.0-gompi-2021a4.9.0-gompi-2022a (D) 4.8.0-gompi-2021a4.9.0-gompi-2022a (D)
newick_utils	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.		newick_utils	Phylogeny Genomics Computer science	10.1093/bioinformatics/btq243				Newick Display 1.6+galaxy1
nextclade	Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.		nextclade	Genomics Sequence analysis Cladistics			MIT		Nextclade 2.7.0+galaxy0
nextflow	Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.		nextflow	Software engineering Workflows Bioinformatics Genomics	Nextflow enables reproducible computational workflows		Apache-2.0			21.04.3 22.04.3			22.10.1
NextPolish	A fast and efficient genome polishing tool for long read assembly. Fast and accurately polish the genome generated by noisy long reads. NextPolish is used to fix base errors (SNV/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both. It contains two core modules, and use a stepwise fashion to correct the error bases in reference genome. To correct the raw third-generation sequencing (TGS) long reads with approximately 15-10% sequencing errors, please use NextDenovo		nextpolish	Sequence assembly Plant biology Mapping	NextPolish: A fast and efficient genome polishing tool for long-read assembly								1.4.1--py311he4a0461_1
NextPolish2	A fast and efficient genome polishing tool for long read assembly. Fast and accurately polish the genome generated by noisy long reads. NextPolish is used to fix base errors (SNV/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both. It contains two core modules, and use a stepwise fashion to correct the error bases in reference genome. To correct the raw third-generation sequencing (TGS) long reads with approximately 15-10% sequencing errors, please use NextDenovo		nextpolish2	Sequence assembly Plant biology Mapping	NextPolish: A fast and efficient genome polishing tool for long-read assembly								0.1.0--hd03093a_0
NGS			ngs										2.10.9-gcccore-10.3.0
ngsutils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets		ngsutils	Genomics Transcriptomics	NGSUtils: A software suite for analyzing and manipulating next-generation sequencing datasets	ngsutils	GPL-3.0		BAM filter 0.5.9
ninja	Nearly Infinite Neighbor Joining Application		ninja	Phylogeny			MIT				0.98-cluster_only		1.10.2-gcccore-10.3.01.10.2-gcccore-11.3.0 (D) 1.10.2-gcccore-10.3.01.10.2-gcccore-11.3.0 (D)
NOVOPlasty			NOVOPlasty						NOVOplasty 4.3.1+galaxy0
nseg			nseg								1.0.1
Nucleotide subsequence search			bg_find_subsequences						Nucleotide subsequence search 0.2
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.		obitools	Sequence analysis DNA Sequencing	obitools: A unix-inspired software package for DNA metabarcoding	OBITools			10 tools Tool Name Description obiannotate 1.2.13 obiannotate: Adds/Edits sequence record annotations obiclean 1.2.13 obiclean: tags a set of sequences for PCR/sequencing errors identification obiconvert 1.2.13 obiconvert: converts sequence files to different output formats obigrep 1.2.13 obigrep: Filters sequence file Illuminapairedend 1.2.13 Illuminapairedend: Construct consensus reads from Illumina pair-end reads NGSfilter 1.2.13 NGSfilter: Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers obisort 1.2.13 obisort: sorts sequence records according to the value of a given attribute obistat 1.2.13 obistat: computes basic statistics for attribute values obitab 1.2.13 obitab: converts sequence file to a tabular file obiuniq 1.2.13 obiuniq:
ont-fast5-api			ont-fast5-api										4.1.1--pyhdfd78af_0
OpenMS	Open source library and a collection of tools and interfaces for the analysis of mass spectrometry data. Includes over 200 standalone (TOPP) tools that can be combined to a workflow with the integrated workflow editor TOPPAS. Raw and intermediate mass spectrometry data can be visualised with the included viewer TOPPView.		openms	Proteomics experiment Proteomics Metabolomics	2 publications Publications OpenMS: A flexible open-source software platform for mass spectrometry data analysis OpenMS and TOPP: open source software for LC-MS data analysis.	OpenMS	BSD-3-Clause		35 tools Tool Name Description TargetedFileConverter 3.1+galaxy0 TargetedFileConverter: Converts different transition files for targeted proteomics / metabolomics analysis XTandemAdapter 2.8+galaxy0 XTandemAdapter: Annotates MS/MS spectra using X! Tandem. XMLValidator 2.8+galaxy0 XMLValidator: Validates XML files against an XSD schema. TextExporter 2.8+galaxy0 TextExporter: Exports various XML formats to a text file. ProteinQuantifier 2.8+galaxy0 ProteinQuantifier: Compute peptide and protein abundances PeptideIndexer 2.8+galaxy0 PeptideIndexer: Refreshes the protein references for all peptide hits. PeakPickerHiRes 2.8+galaxy0 PeakPickerHiRes: Finds mass spectrometric peaks in profile mass spectra. OpenSwathRTNormalizer 2.8+galaxy0 OpenSwathRTNormalizer: This tool will take a description of RT peptides and their normalized retention time to write out a transformation file on how to transform the RT space into the normalized space. OpenSwathMzMLFileCacher 2.8+galaxy0 OpenSwathMzMLFileCacher: This tool caches the spectra and chromatogram data of an mzML to disk. OpenSwathFileSplitter 2.8+galaxy0 OpenSwathFileSplitter: Splits SWATH files into n files, each containing one window. OpenSwathDIAPreScoring 2.8+galaxy0 OpenSwathDIAPreScoring: Scoring spectra using the DIA scores. OpenSwathDecoyGenerator 2.8+galaxy0 OpenSwathDecoyGenerator: Generates decoys according to different models for a specific TraML OpenSwathAssayGenerator 2.8+galaxy0 OpenSwathAssayGenerator: Generates assays according to different models for a specific TraML OpenSwathAnalyzer 2.8+galaxy0 OpenSwathAnalyzer: Picks peaks and finds features in an SWATH-MS or SRM experiment. MzTabExporter 2.8+galaxy0 MzTabExporter: Exports various XML formats to an mzTab file. MultiplexResolver 2.8+galaxy0 MultiplexResolver: Completes peptide multiplets and resolves conflicts within them. MSGFPlusAdapter 2.8+galaxy0 MSGFPlusAdapter: MS/MS database search using MS-GF+. IDScoreSwitcher 2.8+galaxy0 IDScoreSwitcher: Switches between different scores of peptide or protein hits in identification data IDPosteriorErrorProbability 2.8+galaxy0 IDPosteriorErrorProbability: Estimates probabilities for incorrectly assigned peptide sequences and a set of search engine scores using a mixture model. IDMerger 2.8+galaxy0 IDMerger: Merges several protein/peptide identification files into one file. IDMapper 2.8+galaxy0 IDMapper: Assigns protein/peptide identifications to features or consensus features. IDFilter 2.8+galaxy0 IDFilter: Filters results from protein or peptide identification engines based on different criteria. IDConflictResolver 2.8+galaxy0 IDConflictResolver: Resolves ambiguous annotations of features with peptide identifications HighResPrecursorMassCorrector 2.8+galaxy0 HighResPrecursorMassCorrector: Corrects the precursor mass and charge determined by the instrument software. FileConverter 2.8+galaxy0 FileConverter: Converts between different MS file formats. FeatureFinderMultiplex 2.8+galaxy0 FeatureFinderMultiplex: Determination of peak ratios in LC-MS data FalseDiscoveryRate 2.8+galaxy0 FalseDiscoveryRate: Estimates the false discovery rate on peptide and protein level using decoy searches. ConsensusID 2.8+galaxy0 ConsensusID: Computes a consensus of peptide identifications of several identification engines. DecoyDatabase 2.8+galaxy0 DecoyDatabase: Create decoy sequence database from forward sequence database. FidoAdapter 2.8+galaxy0 FidoAdapter: Runs the protein inference engine Fido. FileFilter 2.8+galaxy0 FileFilter: Extracts or manipulates portions of data from peak, feature or consensus-feature files. FileInfo 2.8+galaxy0 FileInfo: Shows basic information about the file, such as data ranges and file type. FileMerger 2.8+galaxy0 FileMerger: Merges several MS files into one file. OpenSwathConfidenceScoring 2.8+galaxy0 OpenSwathConfidenceScoring: Compute confidence scores for OpenSwath results OpenSwathWorkflow 2.8+galaxy0 OpenSwathWorkflow: Complete workflow to run OpenSWATH
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.		orthofinder	Phylogenetics Phylogenomics Bioinformatics Comparative genomics Sequence analysis	2 publications Publications 10.1186/s13059-015-0721-2 10.1101/466201		GPL-3.0		OrthoFinder 2.5.5+galaxy0
PAMPA-Galaxy			pampa						5 tools Tool Name Description Calculate community metrics 0.0.2 Calculate community metrics: calculate community metrics from abundance data Compute GLM on community data 0.0.2 Compute GLM on community data: Compute a GLM of your choice on community data Compute GLM on population data 0.0.2 Compute GLM on population data: Compute a GLM of your choice on population data Create a plot from GLM data 0.0.2 Create a plot from GLM data: as temporal trend Calculate presence absence table 0.0.2 Calculate presence absence table: calculate presence absence table from observation data
pandoc			pandoc										3.1.2
Pangolin	Pangolin is a deep-learning based method for predicting splice site strengths (for details, see Zeng and Li, Genome Biology 2022). It is available as a command-line tool that can be run on a VCF or CSV file containing variants of interest; Pangolin will predict changes in splice site strength due to each variant, and return a file of the same format. Pangolin's models can also be used with custom sequences.		pangolin	RNA splicing Genetic variation Gene transcripts RNA-Seq Exome sequencing	Predicting RNA splicing from DNA sequence using Pangolin		GPL-3.0		Pangolin 4.3+galaxy2
ParaView	ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities.		paraview	Data visualisation Imaging			BSD-3-Clause			5.8.0 5.8.0-mesa 5.8.0-gpu 5.9.1 5.9.1-mesa 5.9.1-gpu 5.10.1 5.9.1-mesa 5.10.1-mesa 5.9.1-gpu
Parse mitochondrial blast			parse_mito_blast						Parse mitochondrial blast 1.0.2+galaxy0
Parse parameter value			param_value_from_file						Parse parameter value 0.1.0
Parsnp	Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible platform for visualizing genome alignments and phylogenetic trees.		parsnp	DNA polymorphism Phylogenetics Structure analysis			BSD-3-Clause						1.7.4--hdcf5f25_2
Pathview	Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.		pathview	Molecular interactions, pathways and networks Systems biology Data visualisation	Pathview: An R/Bioconductor package for pathway-based data integration and visualization	Pathview	GPL-3.0		Pathview 1.34.0+galaxy0
Pavian	Web application for exploring metagenomics classification results, with a special focus on infectious disease diagnosis. Pinpointing pathogens in metagenomics classification results is often complicated by host and laboratory contaminants as well as many non-pathogenic microbiota. Researchers can analyze, display and transform results from the Kraken and Centrifuge classifiers using interactive tables, heatmaps and flow diagrams.		pavian	Metagenomics Model organisms	10.1101/084715		GPL-3.0		Pavian 1.0
pblat	Multithread blat algorithm speeding up aligning sequences to genomes.		pblat	RNA-seq Mapping Gene transcripts	pblat: A multithread blat algorithm speeding up aligning sequences to genomes		Unlicense				2.5
pe_histogram	Productive visualization of high-throughput sequencing data using the SeqCode open portable platform.		pe_histogram	ChIP-seq RNA-Seq Epigenetics Methylated DNA immunoprecipitation Transcription factors and regulatory sites	Productive visualization of high-throughput sequencing data using the SeqCode open portable platform		GPL-3.0		Paired-end histogram 1.0.1
PEAR	Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results.		pear	Sequence assembly	PEAR: A fast and accurate Illumina Paired-End reAd mergeR		CC-BY-NC-1.0		Pear 0.9.6.3				0.9.6--h9d449c0_10
PepPointer			PepPointer						PepPointer 0.1.3+galaxy1
Peptide Genomic Coordinate			peptide_genomic_coordinate						Peptide Genomic Coordinate 1.0.0
Peptide Shaker	PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data		peptideshaker	Proteomics Proteomics experiment Proteome	PeptideShaker enables reanalysis of MS-derived proteomics data sets: To the editor		Apache-2.0		4 tools Tool Name Description FastaCLI 4.0.41+galaxy1 FastaCLI: Appends decoy sequences to FASTA files Identification Parameters 4.0.41+galaxy1 Identification Parameters: Sets the identification parameters to be used in SearchGUI and PeptideShaker apps Peptide Shaker 2.0.33+galaxy1 Peptide Shaker: Perform protein identification using various search engines based on results from SearchGUI Search GUI 4.0.41+galaxy1 Search GUI: Perform protein identification using various search engines and prepare results for input to Peptide Shaker
Percolator	Semi-supervised learning for peptide identification from MS/MS data.		percolator	Proteomics Proteomics experiment Statistics and probability Machine learning	Semi-supervised learning for peptide identification from shotgun proteomics datasets	Percolator			4 tools Tool Name Description Search engine output to Pin converter 3.5+galaxy0 Search engine output to Pin converter: to create Percolator input files Percolator 3.5+galaxy0 Percolator: accurate peptide identification Pout2mzid 0.3.03 Pout2mzid: add Percolator scoring to mzIdentML Create nested list 3.3 Create nested list: based on filenames and batch sizes
perllib			perllib								v5.26.3
PfamScan	This tool is used to search a FASTA sequence against a library of Pfam HMM.		pfamscan	Sequence analysis					PfamScan 1.6+galaxy0
Pharokka	Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes.		pharokka	Metagenomics Sequence sites, features and motifs Workflows Functional, regulatory and non-coding RNA	Pharokka: a fast scalable bacteriophage annotation tool		MIT		pharokka 1.3.2+galaxy0
phinch			phinch						Phinch Visualisation 0.1
PHP			php							5.6.40
Phyloseq	Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.		phyloseq	Microbiology Sequence analysis Metagenomics	Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data	Phyloseq	GPL-3.0		2 tools Tool Name Description Phyloseq Biom Filtering 1.22.3.2 Phyloseq Biom Filtering: biom file filter Phyloseq Ordination Plot 1.22.3.2 Phyloseq Ordination Plot: ordination plotting
PhyML	Phylogenetic estimation software using Maximum Likelihood		phyml	Phylogenetics Bioinformatics Phylogenetics	5 publications Publications 10.1093/sysbio/syq010 10.1080/10635150390235520 10.1093/bioinformatics/bti713 10.1080/10635150600755453 10.1093/nar/gki352	PhyML	GPL-2.0		PhyML 3.3.20220408+galaxy0
PICARD	A set of command line tools for manipulating high-throughput sequencing (HTS) data in formats such as SAM/BAM/CRAM and VCF. Available as a standalone program or within the GATK4 program.		picard	Sequencing Data management		PICARD	MIT		31 tools Tool Name Description FixMateInformation 3.1.1.0 FixMateInformation: ensure that all mate-pair information is in sync between each read and it's mate pair SortSam 3.1.1.0 SortSam: sort SAM/BAM dataset RevertSam 3.1.1.0 RevertSam: revert SAM/BAM datasets to a previous state ReplaceSamHeader 3.1.1.0 ReplaceSamHeader: replace header in a SAM/BAM dataset MarkDuplicates 3.1.1.0 MarkDuplicates: examine aligned records in BAM datasets to locate duplicate molecules CleanSam 3.1.1.0 CleanSam: perform SAM/BAM grooming CollectHsMetrics 3.1.1 CollectHsMetrics: compute metrics about datasets generated through hybrid-selection (e.g. exome) AddCommentsToBam 3.1.1.0 AddCommentsToBam: add comments to BAM dataset ValidateSamFile 3.1.1.0 ValidateSamFile: assess validity of SAM/BAM dataset ReorderSam 3.1.1.0 ReorderSam: reorder reads to match ordering in reference sequences MeanQualityByCycle 3.1.1.0 MeanQualityByCycle: chart distribution of base qualities Picard Collect Sequencing Artifact Metrics 3.1.1.0 Picard Collect Sequencing Artifact Metrics: Collect metrics to quantify single-base sequencing artifacts RevertOriginalBaseQualitiesAndAddMateCigar 3.1.1.0 RevertOriginalBaseQualitiesAndAddMateCigar: revert the original base qualities and add the mate cigar tag BedToIntervalList 3.1.1.0 BedToIntervalList: convert coordinate data into picard interval list format MergeBamAlignment 3.1.1.0 MergeBamAlignment: merge alignment data with additional info stored in an unmapped BAM dataset QualityScoreDistribution 3.1.1.0 QualityScoreDistribution: chart quality score distribution MarkDuplicatesWithMateCigar 3.1.1.0 MarkDuplicatesWithMateCigar: examine aligned records in BAM datasets to locate duplicate molecules Downsample SAM/BAM 3.1.1.0 Downsample SAM/BAM: Downsample a file to retain a subset of the reads MergeSamFiles 3.1.1.0 MergeSamFiles: merges multiple SAM/BAM datasets into one SamToFastq 3.1.1.0 SamToFastq: extract reads and qualities from SAM/BAM dataset and convert to fastq CollectGcBiasMetrics 3.1.1.0 CollectGcBiasMetrics: charts the GC bias metrics Collect Alignment Summary Metrics 3.1.1.0 Collect Alignment Summary Metrics: writes a file containing summary alignment metrics CollectInsertSizeMetrics 3.1.1.0 CollectInsertSizeMetrics: plots distribution of insert sizes CollectRnaSeqMetrics 3.1.1.0 CollectRnaSeqMetrics: collect metrics about the alignment of RNA to various functional classes of loci in the genome NormalizeFasta 3.1.1.0 NormalizeFasta: normalize fasta datasets AddOrReplaceReadGroups 3.1.1.0 AddOrReplaceReadGroups: add or replaces read group information FastqToSam 3.1.1.0 FastqToSam: convert Fastq data into unaligned BAM FilterSamReads 3.1.1.0 FilterSamReads: include or exclude aligned and unaligned reads and read lists CollectBaseDistributionByCycle 3.1.1.0 CollectBaseDistributionByCycle: charts the nucleotide distribution per cycle in a SAM or BAM dataset CollectWgsMetrics 3.1.1.0 CollectWgsMetrics: compute metrics for evaluating of whole genome sequencing experiments EstimateLibraryComplexity 3.1.1.0 EstimateLibraryComplexity: assess sequence library complexity from read sequences		2.27.43.1.1 2.27.43.1.1		2.25.1-java-11
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.		picrust	Metagenomics Microbial ecology Functional, regulatory and non-coding RNA Metagenomic sequencing	Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences				6 tools Tool Name Description Categorize 1.1.1.0 Categorize: by collapsing hierarchical data to a specified functional level Compare BIOM tables 1.1.1.1 Compare BIOM tables: Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples. Format 1.1.1.0 Format: tree and trait tables Metagenome Contributions 1.1.1.0 Metagenome Contributions: of OTUs to user-specified functions Normalize 1.1.1.1 Normalize: the relative abundance of each OTU by the predicted number of 16S copies Predict Metagenome 1.1.1.0 Predict Metagenome: based on the abundance of OTUs and a functional database
PICRUSt 2	PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.		picrust2	Metagenomics Microbiology Phylogenetics Metagenomic sequencing	10.1038/s41587-020-0548-6		GPL-3.0		7 tools Tool Name Description PICRUSt2 Generation of shuffled predictions 2.5.3+galaxy0 PICRUSt2 Generation of shuffled predictions: for a specified number of replicates PICRUSt2 Sequence placement 2.5.3+galaxy0 PICRUSt2 Sequence placement: into reference tree PICRUSt2 Pathway abundance inference 2.5.3+galaxy0 PICRUSt2 Pathway abundance inference: PICRUSt2 Metagenome prediction 2.5.3+galaxy0 PICRUSt2 Metagenome prediction: to generate per-sample metagenome functional profiles based on the predicted functions for each study sequence PICRUSt2 Hidden state prediction (HSP) 2.5.3+galaxy0 PICRUSt2 Hidden state prediction (HSP): to predict gene family abundances PICRUSt2 Add descriptions 2.5.3+galaxy0 PICRUSt2 Add descriptions: column to a function abundance table PICRUSt2 Full pipeline 2.5.3+galaxy0 PICRUSt2 Full pipeline:
Pileup-to-Interval			pileup_interval						Pileup-to-Interval 1.0.3
Pilon	Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies.		pilon	Assembly	Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement	Pilon			pilon 1.20.1
pipe_t	PIPE-T is a Galaxy Workflow for processing and analyzing miR expression profiles by RTqPCR. It is a tool that offers several state-of-the-art options for parsing, filtering, normalizing, imputing and analyzing RT-qPCR expression data. Integration of PIPE-T into Galaxy allows experimentalists with strong bioinformatic background, as well as those without any programming or development expertise, to perform complex analysis in a simple to use, transparent, accessible, reproducible, and user-friendly environment		pipe_t	PCR experiment Transcriptomics Biomarkers Microarray experiment	PIPE-T: a new Galaxy tool for the analysis of RT-qPCR expression data		MIT		PIPE-T 1.0
PlasFlow	PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.		PlasFlow	Metagenomics			GPL-3.0		PlasFlow 1.1.0+galaxy0
PlasmidFinder	PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).		plasmidfinder	Whole genome sequencing Sequence assembly Mapping Probes and primers	PlasmidFinder and In Silico pMLST: Identification and Typing of Plasmid Replicons in Whole-Genome Sequencing (WGS)				PlasmidFinder 2.1.6+galaxy1
plink	Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.		plink	GWAS study	PLINK: A tool set for whole-genome association and population-based linkage analyses	plink	GPL-2.0				v2.00a3.7		2.00a3.6-gcc-11.3.0
PnetCDF	PnetCDF: A Parallel I/O Library for NetCDF File Access		pnetcdf	Computer science	10.1109/SC.2003.10053		Freeware			1.11.2
Poisson two-sample test			poisson2test						Poisson two-sample test 1.0.0
porechop			porechop						Porechop 0.2.4+galaxy0
poretools	Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.		poretools	DNA Sequencing	Poretools: A toolkit for analyzing nanopore sequence data	poretools			13 tools Tool Name Description Extract nanopore events 0.6.1a1.1 Extract nanopore events: from a set of sequencing reads Extract reads 0.6.1a1.0 Extract reads: in FASTA or FASTQ format from nanopore files Generate histogram 0.6.1a1.1 Generate histogram: of nanopore read lengths Show nucleotide 0.6.1a1.0 Show nucleotide: distribution in nanopore sequencing reads Plot performance 0.6.1a1.1 Plot performance: per cell in nanopore reads Show quality 0.6.1a1.0 Show quality: score distribution in nanopore sequencing reads Generate box-whisker 0.6.1a1.1 Generate box-whisker: plot of quality score distribution over positions in nanopore reads Plot signals 0.6.1a1.1 Plot signals: for nanopore reads Read length statistics 0.6.1a1.0 Read length statistics: from a set of FAST5 files Extract FASTQ 0.6.1a1.0 Extract FASTQ: in tabular format from a set of FAST5 files Extract time 0.6.1a1.0 Extract time: and channel information from a set of FAST5 files Get longest read 0.6.1a1.0 Get longest read: from a set of FAST5 files. Collector’s curve 0.6.1a1.1 Collector’s curve: of sequencing yield over time
pplacer	Tools for performing taxonomic assignment based on phylogeny using pplacer and clst.		pplacer	Taxonomy	Orchestrating high-throughput genomic analysis with Bioconductor	pplacer	GPL-3.0						1.1.alpha19
PretextMap			pretext_map						PretextMap 0.1.9+galaxy1
PretextView / Pretext Suite	Pretext is an OpenGL-powered pretext contact map viewer.		pretextview	Mapping			MIT		Pretext Snapshot 0.0.3+galaxy2
Prodigal	The pipeline runs PRODIGAL gene predictions on all genomes, runs pan-reciprocal BLAST, and identifies ortholog sets. For a set of orthologous genes, if the positions of the PRODIGAL selected starts coincide in a multiple sequence alignment, they are accepted. If they do not coincide, a consistent start position is sought where a majority of the highest-scoring PRODIGAL selected sites coincide. If such a position is found, it is accepted, and the predictions are changed for the outlying genes.		prodigal	DNA Sequence analysis Nucleic acid sites, features and motifs	Genome majority vote improves gene predictions						2.6.3		2.6.3-gcccore-10.3.02.6.3-gcccore-11.3.0 (D) 2.6.3-gcccore-10.3.02.6.3-gcccore-11.3.0 (D)
proFIA	Flow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA-HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the package that implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) and generates the peak table.		profia	Metabolomics	Orchestrating high-throughput genomic analysis with Bioconductor		CECILL-2.1		proFIA 3.1.0
progressbar2			progressbar2								4.2.0
Prokka	Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.		prokka	Genomics Model organisms Virology	10.1093/bioinformatics/btu153	Prokka			Prokka 1.14.6+galaxy1				1.14.5-gompi-2021a1.14.5-gompi-2022a (D) 1.14.5-gompi-2021a1.14.5-gompi-2022a (D)
pslcdnafilter			pslcdnafilter								0
Purge_Dups	Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences		purge_dups	Sequence assembly	10.1101/729962		MIT		Purge overlaps 1.2.6+galaxy0
pybigwig			pybigwig										0.3.18-foss-2021a0.3.18-foss-2022a (D) 0.3.18-foss-2021a0.3.18-foss-2022a (D)
pycoqc	PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data.		pycoqc	Sequence analysis Data quality management Sequencing			GPL-3.0		Pycoqc 2.5.2+galaxy0				2.5.2-foss-2021a
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:.		pygenometracks	Model organisms Imaging Workflows	pyGenomeTracks: reproducible plots for multivariate genomic datasets		GPL-3.0		pyGenomeTracks 3.8+galaxy2
pyprophet			pyprophet						4 tools Tool Name Description PyProphet merge 2.1.4.0 PyProphet merge: Merge multiple osw files PyProphet peptide 2.1.4.0 PyProphet peptide: Peptide error-rate estimation PyProphet protein 2.1.4.0 PyProphet protein: Protein error-rate estimation PyProphet score 2.1.4.2 PyProphet score: Error-rate estimation for MS1, MS2 and transition-level data
pysam	A Python module for reading and manipulating SAM/BAM/VCF/BCF files.		pysam	Sequencing Mapping	The Sequence Alignment/Map format and SAMtools		MIT						0.16.0.1-gcc-10.3.00.19.1-gcc-11.3.0 (D) 0.16.0.1-gcc-10.3.00.19.1-gcc-11.3.0 (D)
PyTorch	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.		pytorch	Machine learning Computer science			BSD-3-Clause			1.4.0a0 1.5.1 1.9.0 1.10.0 1.12.1
QIIME2.0	QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.		qiime2	Microbial ecology Phylogeny Metatranscriptomics Metagenomics	Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2		BSD-3-Clause		161 tools Tool Name Description qiime2 tools import 2023.5.0+dist.h193f7cc9.3 qiime2 tools import: Import data into a QIIME 2 artifact qiime2 alignment mafft-add 2023.5.0+q2galaxy.2023.5.0.2 qiime2 alignment mafft-add: Add sequences to multiple sequence alignment with MAFFT. qiime2 alignment mafft 2023.5.0+q2galaxy.2023.5.0.2 qiime2 alignment mafft: De novo multiple sequence alignment with MAFFT qiime2 alignment mask 2023.5.0+q2galaxy.2023.5.0.2 qiime2 alignment mask: Positional conservation and gap filtering. qiime2 composition add-pseudocount 2023.5.0+q2galaxy.2023.5.0.2 qiime2 composition add-pseudocount: Add pseudocount to table. qiime2 composition ancom 2023.5.0+q2galaxy.2023.5.0.2 qiime2 composition ancom: Apply ANCOM to identify features that differ in abundance. qiime2 composition tabulate 2023.5.0+q2galaxy.2023.5.0.2 qiime2 composition tabulate: View tabular output from ANCOM-BC. qiime2 tools export 2023.5.0+dist.h193f7cc9.2 qiime2 tools export: Export data from a QIIME 2 artifact qiime2 cutadapt demux-paired 2023.5.1+q2galaxy.2023.5.0.2 qiime2 cutadapt demux-paired: Demultiplex paired-end sequence data with barcodes in-sequence. qiime2 cutadapt demux-single 2023.5.1+q2galaxy.2023.5.0.2 qiime2 cutadapt demux-single: Demultiplex single-end sequence data with barcodes in-sequence. qiime2 cutadapt trim-paired 2023.5.1+q2galaxy.2023.5.0.2 qiime2 cutadapt trim-paired: Find and remove adapters in demultiplexed paired-end sequences. qiime2 cutadapt trim-single 2023.5.1+q2galaxy.2023.5.0.2 qiime2 cutadapt trim-single: Find and remove adapters in demultiplexed single-end sequences. qiime2 dada2 denoise-ccs 2023.5.0+q2galaxy.2023.5.0.2 qiime2 dada2 denoise-ccs: Denoise and dereplicate single-end Pacbio CCS qiime2 dada2 denoise-paired 2023.5.0+q2galaxy.2023.5.0.2 qiime2 dada2 denoise-paired: Denoise and dereplicate paired-end sequences qiime2 dada2 denoise-pyro 2023.5.0+q2galaxy.2023.5.0.2 qiime2 dada2 denoise-pyro: Denoise and dereplicate single-end pyrosequences qiime2 dada2 denoise-single 2023.5.0+q2galaxy.2023.5.0.2 qiime2 dada2 denoise-single: Denoise and dereplicate single-end sequences qiime2 deblur denoise-16S 2023.5.0+q2galaxy.2023.5.0.2 qiime2 deblur denoise-16S: Deblur sequences using a 16S positive filter. qiime2 deblur denoise-other 2023.5.0+q2galaxy.2023.5.0.2 qiime2 deblur denoise-other: Deblur sequences using a user-specified positive filter. qiime2 deblur visualize-stats 2023.5.0+q2galaxy.2023.5.0.2 qiime2 deblur visualize-stats: Visualize Deblur stats per sample. qiime2 demux emp-paired 2023.5.0+q2galaxy.2023.5.0.2 qiime2 demux emp-paired: Demultiplex paired-end sequence data generated with the EMP protocol. qiime2 demux emp-single 2023.5.0+q2galaxy.2023.5.0.2 qiime2 demux emp-single: Demultiplex sequence data generated with the EMP protocol. qiime2 demux filter-samples 2023.5.0+q2galaxy.2023.5.0.2 qiime2 demux filter-samples: Filter samples out of demultiplexed data. qiime2 demux subsample-paired 2023.5.0+q2galaxy.2023.5.0.2 qiime2 demux subsample-paired: Subsample paired-end sequences without replacement. qiime2 demux subsample-single 2023.5.0+q2galaxy.2023.5.0.2 qiime2 demux subsample-single: Subsample single-end sequences without replacement. qiime2 demux summarize 2023.5.0+q2galaxy.2023.5.0.2 qiime2 demux summarize: Summarize counts per sample. qiime2 diversity adonis 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity adonis: adonis PERMANOVA test for beta group significance qiime2 diversity alpha-correlation 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity alpha-correlation: Alpha diversity correlation qiime2 diversity alpha-group-significance 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity alpha-group-significance: Alpha diversity comparisons qiime2 diversity alpha 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity alpha: Alpha diversity qiime2 diversity alpha-phylogenetic 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity alpha-phylogenetic: Alpha diversity (phylogenetic) qiime2 diversity alpha-rarefaction 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity alpha-rarefaction: Alpha rarefaction curves qiime2 diversity beta-correlation 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity beta-correlation: Beta diversity correlation qiime2 diversity beta-group-significance 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity beta-group-significance: Beta diversity group significance qiime2 diversity beta 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity beta: Beta diversity qiime2 diversity beta-phylogenetic 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity beta-phylogenetic: Beta diversity (phylogenetic) qiime2 diversity beta-rarefaction 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity beta-rarefaction: Beta diversity rarefaction qiime2 diversity bioenv 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity bioenv: bioenv qiime2 diversity core-metrics 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity core-metrics: Core diversity metrics (non-phylogenetic) qiime2 diversity core-metrics-phylogenetic 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity core-metrics-phylogenetic: Core diversity metrics (phylogenetic and non-phylogenetic) qiime2 diversity filter-distance-matrix 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity filter-distance-matrix: Filter samples from a distance matrix. qiime2 diversity-lib alpha-passthrough 2023.5.0+q2galaxy.2023.5.0.2 qiime2 diversity-lib alpha-passthrough: Alpha Passthrough (non-phylogenetic) qiime2 diversity-lib beta-passthrough 2023.5.0+q2galaxy.2023.5.0.2 qiime2 diversity-lib beta-passthrough: Beta Passthrough (non-phylogenetic) qiime2 diversity-lib beta-phylogenetic-meta-passthrough 2023.5.0+q2galaxy.2023.5.0.2 qiime2 diversity-lib beta-phylogenetic-meta-passthrough: Beta Phylogenetic Meta Passthrough qiime2 diversity-lib beta-phylogenetic-passthrough 2023.5.0+q2galaxy.2023.5.0.2 qiime2 diversity-lib beta-phylogenetic-passthrough: Beta Phylogenetic Passthrough qiime2 diversity-lib faith-pd 2023.5.0+q2galaxy.2023.5.0.2 qiime2 diversity-lib faith-pd: Faith's Phylogenetic Diversity qiime2 diversity-lib jaccard 2023.5.0+q2galaxy.2023.5.0.2 qiime2 diversity-lib jaccard: Jaccard Distance qiime2 diversity-lib observed-features 2023.5.0+q2galaxy.2023.5.0.2 qiime2 diversity-lib observed-features: Observed Features qiime2 diversity-lib pielou-evenness 2023.5.0+q2galaxy.2023.5.0.2 qiime2 diversity-lib pielou-evenness: Pielou's Evenness qiime2 diversity-lib shannon-entropy 2023.5.0+q2galaxy.2023.5.0.2 qiime2 diversity-lib shannon-entropy: Shannon's Entropy qiime2 diversity-lib unweighted-unifrac 2023.5.0+q2galaxy.2023.5.0.2 qiime2 diversity-lib unweighted-unifrac: Unweighted Unifrac qiime2 diversity-lib weighted-unifrac 2023.5.0+q2galaxy.2023.5.0.2 qiime2 diversity-lib weighted-unifrac: Weighted Unifrac qiime2 diversity mantel 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity mantel: Apply the Mantel test to two distance matrices qiime2 diversity pcoa-biplot 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity pcoa-biplot: Principal Coordinate Analysis Biplot qiime2 diversity pcoa 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity pcoa: Principal Coordinate Analysis qiime2 diversity procrustes-analysis 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity procrustes-analysis: Procrustes Analysis qiime2 diversity tsne 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity tsne: t-distributed stochastic neighbor embedding qiime2 diversity umap 2023.5.1+q2galaxy.2023.5.0.2 qiime2 diversity umap: Uniform Manifold Approximation and Projection qiime2 emperor biplot 2023.5.0+q2galaxy.2023.5.0.2 qiime2 emperor biplot: Visualize and Interact with Principal Coordinates Analysis Biplot qiime2 emperor plot 2023.5.0+q2galaxy.2023.5.0.2 qiime2 emperor plot: Visualize and Interact with Principal Coordinates Analysis Plots qiime2 emperor procrustes-plot 2023.5.0+q2galaxy.2023.5.0.2 qiime2 emperor procrustes-plot: Visualize and Interact with a procrustes plot qiime2 feature-classifier blast 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-classifier blast: BLAST+ local alignment search. qiime2 feature-classifier classify-consensus-blast 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-classifier classify-consensus-blast: BLAST+ consensus taxonomy classifier qiime2 feature-classifier classify-consensus-vsearch 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-classifier classify-consensus-vsearch: VSEARCH-based consensus taxonomy classifier qiime2 feature-classifier classify-hybrid-vsearch-sklearn 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-classifier classify-hybrid-vsearch-sklearn: ALPHA Hybrid classifier: VSEARCH exact match + sklearn classifier qiime2 feature-classifier classify-sklearn 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-classifier classify-sklearn: Pre-fitted sklearn-based taxonomy classifier qiime2 feature-classifier extract-reads 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-classifier extract-reads: Extract reads from reference sequences. qiime2 feature-classifier find-consensus-annotation 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-classifier find-consensus-annotation: Find consensus among multiple annotations. qiime2 feature-classifier fit-classifier-naive-bayes 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-classifier fit-classifier-naive-bayes: Train the naive_bayes classifier qiime2 feature-classifier fit-classifier-sklearn 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-classifier fit-classifier-sklearn: Train an almost arbitrary scikit-learn classifier qiime2 feature-classifier vsearch-global 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-classifier vsearch-global: VSEARCH global alignment search qiime2 feature-table core-features 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table core-features: Identify core features in table qiime2 feature-table filter-features-conditionally 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table filter-features-conditionally: Filter features from a table based on abundance and prevalence qiime2 feature-table filter-samples 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table filter-samples: Filter samples from table qiime2 feature-table filter-seqs 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table filter-seqs: Filter features from sequences qiime2 feature-table group 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table group: Group samples or features by a metadata column qiime2 feature-table heatmap 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table heatmap: Generate a heatmap representation of a feature table qiime2 feature-table merge 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table merge: Combine multiple tables qiime2 feature-table merge-seqs 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table merge-seqs: Combine collections of feature sequences qiime2 feature-table merge-taxa 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table merge-taxa: Combine collections of feature taxonomies qiime2 feature-table presence-absence 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table presence-absence: Convert to presence/absence qiime2 feature-table rarefy 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table rarefy: Rarefy table qiime2 feature-table relative-frequency 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table relative-frequency: Convert to relative frequencies qiime2 feature-table rename-ids 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table rename-ids: Renames sample or feature ids in a table qiime2 feature-table subsample 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table subsample: Subsample table qiime2 feature-table summarize 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table summarize: Summarize table qiime2 feature-table tabulate-seqs 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table tabulate-seqs: View sequence associated with each feature qiime2 feature-table transpose 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table transpose: Transpose a feature table. qiime2 fragment-insertion classify-otus-experimental 2023.5.0+q2galaxy.2023.5.0.2 qiime2 fragment-insertion classify-otus-experimental: Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny. qiime2 fragment-insertion filter-features 2023.5.0+q2galaxy.2023.5.0.2 qiime2 fragment-insertion filter-features: Filter fragments in tree from table. qiime2 fragment-insertion sepp 2023.5.0+q2galaxy.2023.5.0.2 qiime2 fragment-insertion sepp: Insert fragment sequences using SEPP into reference phylogenies. qiime2 gneiss assign-ids 2023.5.0+q2galaxy.2023.5.0.2 qiime2 gneiss assign-ids: Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns. qiime2 gneiss correlation-clustering 2023.5.0+q2galaxy.2023.5.0.2 qiime2 gneiss correlation-clustering: Hierarchical clustering using feature correlation. qiime2 gneiss dendrogram-heatmap 2023.5.0+q2galaxy.2023.5.0.2 qiime2 gneiss dendrogram-heatmap: Dendrogram heatmap. qiime2 gneiss gradient-clustering 2023.5.0+q2galaxy.2023.5.0.2 qiime2 gneiss gradient-clustering: Hierarchical clustering using gradient information. qiime2 gneiss ilr-hierarchical 2023.5.0+q2galaxy.2023.5.0.2 qiime2 gneiss ilr-hierarchical: Isometric Log-ratio Transform applied to a hierarchical clustering qiime2 gneiss ilr-phylogenetic-differential 2023.5.0+q2galaxy.2023.5.0.2 qiime2 gneiss ilr-phylogenetic-differential: Differentially abundant Phylogenetic Log Ratios. qiime2 gneiss ilr-phylogenetic 2023.5.0+q2galaxy.2023.5.0.2 qiime2 gneiss ilr-phylogenetic: Isometric Log-ratio Transform applied to a phylogenetic tree qiime2 gneiss ilr-phylogenetic-ordination 2023.5.0+q2galaxy.2023.5.0.2 qiime2 gneiss ilr-phylogenetic-ordination: Ordination through a phylogenetic Isometric Log Ratio transform. qiime2 longitudinal anova 2023.5.0+q2galaxy.2023.5.0.2 qiime2 longitudinal anova: ANOVA test qiime2 longitudinal feature-volatility 2023.5.0+q2galaxy.2023.5.0.2 qiime2 longitudinal feature-volatility: Feature volatility analysis qiime2 longitudinal first-differences 2023.5.0+q2galaxy.2023.5.0.2 qiime2 longitudinal first-differences: Compute first differences or difference from baseline between sequential states qiime2 longitudinal first-distances 2023.5.0+q2galaxy.2023.5.0.2 qiime2 longitudinal first-distances: Compute first distances or distance from baseline between sequential states qiime2 longitudinal linear-mixed-effects 2023.5.0+q2galaxy.2023.5.0.2 qiime2 longitudinal linear-mixed-effects: Linear mixed effects modeling qiime2 longitudinal maturity-index 2023.5.0+q2galaxy.2023.5.0.2 qiime2 longitudinal maturity-index: Microbial maturity index prediction. qiime2 longitudinal nmit 2023.5.0+q2galaxy.2023.5.0.2 qiime2 longitudinal nmit: Nonparametric microbial interdependence test qiime2 longitudinal pairwise-differences 2023.5.0+q2galaxy.2023.5.0.2 qiime2 longitudinal pairwise-differences: Paired difference testing and boxplots qiime2 longitudinal pairwise-distances 2023.5.0+q2galaxy.2023.5.0.2 qiime2 longitudinal pairwise-distances: Paired pairwise distance testing and boxplots qiime2 longitudinal plot-feature-volatility 2023.5.0+q2galaxy.2023.5.0.2 qiime2 longitudinal plot-feature-volatility: Plot longitudinal feature volatility and importances qiime2 longitudinal volatility 2023.5.0+q2galaxy.2023.5.0.2 qiime2 longitudinal volatility: Generate interactive volatility plot qiime2 metadata distance-matrix 2023.5.0+q2galaxy.2023.5.0.2 qiime2 metadata distance-matrix: Create a distance matrix from a numeric Metadata column qiime2 metadata shuffle-groups 2023.5.0+q2galaxy.2023.5.0.2 qiime2 metadata shuffle-groups: Shuffle values in a categorical sample metadata column. qiime2 metadata tabulate 2023.5.0+q2galaxy.2023.5.0.2 qiime2 metadata tabulate: Interactively explore Metadata in an HTML table qiime2 phylogeny align-to-tree-mafft-fasttree 2023.5.0+q2galaxy.2023.5.0.2 qiime2 phylogeny align-to-tree-mafft-fasttree: Build a phylogenetic tree using fasttree and mafft alignment qiime2 phylogeny align-to-tree-mafft-iqtree 2023.5.0+q2galaxy.2023.5.0.2 qiime2 phylogeny align-to-tree-mafft-iqtree: Build a phylogenetic tree using iqtree and mafft alignment. qiime2 phylogeny align-to-tree-mafft-raxml 2023.5.0+q2galaxy.2023.5.0.2 qiime2 phylogeny align-to-tree-mafft-raxml: Build a phylogenetic tree using raxml and mafft alignment. qiime2 phylogeny fasttree 2023.5.0+q2galaxy.2023.5.0.2 qiime2 phylogeny fasttree: Construct a phylogenetic tree with FastTree. qiime2 phylogeny filter-table 2023.5.0+q2galaxy.2023.5.0.2 qiime2 phylogeny filter-table: Remove features from table if they're not present in tree. qiime2 phylogeny filter-tree 2023.5.0+q2galaxy.2023.5.0.2 qiime2 phylogeny filter-tree: Remove features from tree based on metadata qiime2 phylogeny iqtree 2023.5.0+q2galaxy.2023.5.0.2 qiime2 phylogeny iqtree: Construct a phylogenetic tree with IQ-TREE. qiime2 phylogeny iqtree-ultrafast-bootstrap 2023.5.0+q2galaxy.2023.5.0.2 qiime2 phylogeny iqtree-ultrafast-bootstrap: Construct a phylogenetic tree with IQ-TREE with bootstrap supports. qiime2 phylogeny midpoint-root 2023.5.0+q2galaxy.2023.5.0.2 qiime2 phylogeny midpoint-root: Midpoint root an unrooted phylogenetic tree. qiime2 phylogeny raxml 2023.5.0+q2galaxy.2023.5.0.2 qiime2 phylogeny raxml: Construct a phylogenetic tree with RAxML. qiime2 phylogeny raxml-rapid-bootstrap 2023.5.0+q2galaxy.2023.5.0.2 qiime2 phylogeny raxml-rapid-bootstrap: Construct a phylogenetic tree with bootstrap supports using RAxML. qiime2 phylogeny robinson-foulds 2023.5.0+q2galaxy.2023.5.0.2 qiime2 phylogeny robinson-foulds: Calculate Robinson-Foulds distance between phylogenetic trees. qiime2 quality-control bowtie2-build 2023.5.0+q2galaxy.2023.5.0.2 qiime2 quality-control bowtie2-build: Build bowtie2 index from reference sequences. qiime2 quality-control evaluate-composition 2023.5.0+q2galaxy.2023.5.0.2 qiime2 quality-control evaluate-composition: Evaluate expected vs. observed taxonomic composition of samples qiime2 quality-control evaluate-seqs 2023.5.0+q2galaxy.2023.5.0.2 qiime2 quality-control evaluate-seqs: Compare query (observed) vs. reference (expected) sequences. qiime2 quality-control evaluate-taxonomy 2023.5.0+q2galaxy.2023.5.0.2 qiime2 quality-control evaluate-taxonomy: Evaluate expected vs. observed taxonomic assignments qiime2 quality-control exclude-seqs 2023.5.0+q2galaxy.2023.5.0.2 qiime2 quality-control exclude-seqs: Exclude sequences by alignment qiime2 quality-control filter-reads 2023.5.0+q2galaxy.2023.5.0.2 qiime2 quality-control filter-reads: Filter demultiplexed sequences by alignment to reference database. qiime2 quality-filter q-score 2023.5.0+q2galaxy.2023.5.0.2 qiime2 quality-filter q-score: Quality filter based on sequence quality scores. qiime2 sample-classifier classify-samples-from-dist 2023.5.0+q2galaxy.2023.5.0.2 qiime2 sample-classifier classify-samples-from-dist: Run k-nearest-neighbors on a labeled distance matrix. qiime2 sample-classifier classify-samples 2023.5.0+q2galaxy.2023.5.0.2 qiime2 sample-classifier classify-samples: Train and test a cross-validated supervised learning classifier. qiime2 sample-classifier classify-samples-ncv 2023.5.0+q2galaxy.2023.5.0.2 qiime2 sample-classifier classify-samples-ncv: Nested cross-validated supervised learning classifier. qiime2 sample-classifier confusion-matrix 2023.5.0+q2galaxy.2023.5.0.2 qiime2 sample-classifier confusion-matrix: Make a confusion matrix from sample classifier predictions. qiime2 sample-classifier fit-classifier 2023.5.0+q2galaxy.2023.5.0.2 qiime2 sample-classifier fit-classifier: Fit a supervised learning classifier. qiime2 sample-classifier fit-regressor 2023.5.0+q2galaxy.2023.5.0.2 qiime2 sample-classifier fit-regressor: Fit a supervised learning regressor. qiime2 sample-classifier heatmap 2023.5.0+q2galaxy.2023.5.0.2 qiime2 sample-classifier heatmap: Generate heatmap of important features. qiime2 sample-classifier metatable 2023.5.0+q2galaxy.2023.5.0.2 qiime2 sample-classifier metatable: Convert (and merge) positive numeric metadata (in)to feature table. qiime2 sample-classifier predict-classification 2023.5.0+q2galaxy.2023.5.0.2 qiime2 sample-classifier predict-classification: Use trained classifier to predict target values for new samples. qiime2 sample-classifier predict-regression 2023.5.0+q2galaxy.2023.5.0.2 qiime2 sample-classifier predict-regression: Use trained regressor to predict target values for new samples. qiime2 sample-classifier regress-samples 2023.5.0+q2galaxy.2023.5.0.2 qiime2 sample-classifier regress-samples: Train and test a cross-validated supervised learning regressor. qiime2 sample-classifier regress-samples-ncv 2023.5.0+q2galaxy.2023.5.0.2 qiime2 sample-classifier regress-samples-ncv: Nested cross-validated supervised learning regressor. qiime2 sample-classifier scatterplot 2023.5.0+q2galaxy.2023.5.0.2 qiime2 sample-classifier scatterplot: Make 2D scatterplot and linear regression of regressor predictions. qiime2 sample-classifier split-table 2023.5.0+q2galaxy.2023.5.0.2 qiime2 sample-classifier split-table: Split a feature table into training and testing sets. qiime2 sample-classifier summarize 2023.5.0+q2galaxy.2023.5.0.2 qiime2 sample-classifier summarize: Summarize parameter and feature extraction information for a trained estimator. qiime2 taxa barplot 2023.5.0+q2galaxy.2023.5.0.2 qiime2 taxa barplot: Visualize taxonomy with an interactive bar plot qiime2 taxa collapse 2023.5.0+q2galaxy.2023.5.0.2 qiime2 taxa collapse: Collapse features by their taxonomy at the specified level qiime2 taxa filter-seqs 2023.5.0+q2galaxy.2023.5.0.2 qiime2 taxa filter-seqs: Taxonomy-based feature sequence filter. qiime2 taxa filter-table 2023.5.0+q2galaxy.2023.5.0.2 qiime2 taxa filter-table: Taxonomy-based feature table filter. qiime2 vsearch cluster-features-closed-reference 2023.5.0+q2galaxy.2023.5.0.2 qiime2 vsearch cluster-features-closed-reference: Closed-reference clustering of features. qiime2 vsearch cluster-features-de-novo 2023.5.0+q2galaxy.2023.5.0.2 qiime2 vsearch cluster-features-de-novo: De novo clustering of features. qiime2 vsearch cluster-features-open-reference 2023.5.0+q2galaxy.2023.5.0.2 qiime2 vsearch cluster-features-open-reference: Open-reference clustering of features. qiime2 vsearch dereplicate-sequences 2023.5.0+q2galaxy.2023.5.0.2 qiime2 vsearch dereplicate-sequences: Dereplicate sequences. qiime2 vsearch fastq-stats 2023.5.0+q2galaxy.2023.5.0.2 qiime2 vsearch fastq-stats: Fastq stats with vsearch. qiime2 vsearch merge-pairs 2023.5.0+q2galaxy.2023.5.0.2 qiime2 vsearch merge-pairs: Merge paired-end reads. qiime2 vsearch uchime-denovo 2023.5.0+q2galaxy.2023.5.0.2 qiime2 vsearch uchime-denovo: De novo chimera filtering with vsearch. qiime2 vsearch uchime-ref 2023.5.0+q2galaxy.2023.5.0.2 qiime2 vsearch uchime-ref: Reference-based chimera filtering with vsearch. qiime2 composition ancombc 2023.5.0+q2galaxy.2023.5.0.2 qiime2 composition ancombc: Analysis of Composition of Microbiomes with Bias Correction qiime2 diversity-lib bray-curtis 2023.5.0+q2galaxy.2023.5.0.2 qiime2 diversity-lib bray-curtis: Bray-Curtis Dissimilarity qiime2 feature-table filter-features 2023.5.0+q2galaxy.2023.5.0.2 qiime2 feature-table filter-features: Filter features from table				2022.8
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.		qualimap	Data quality management	22914218	qualimap			4 tools Tool Name Description QualiMap Multi-Sample BamQC 2.3+galaxy0 QualiMap Multi-Sample BamQC: QualiMap BamQC 2.3+galaxy0 QualiMap BamQC: QualiMap Counts QC 2.3+galaxy0 QualiMap Counts QC: QualiMap RNA-Seq QC 2.2.2d+galaxy1 QualiMap RNA-Seq QC:
quasitools	A Collection of Tools for Viral Quasispecies Analysis | Abstract Summary quasitools is a collection of newly-developed, open-source tools for analyzing viral quasispcies data. The application suite includes tools with the ability to create consensus sequences, call nucleotide, codon, and amino acid variants, calculate the complexity of a quasispecies, and measure the genetic distance between two similar quasispecies. These tools may be run independently or in user-created workflows. Availability The quasitools suite is a freely available application licensed under the Apache License, Version 2.0. The source code, documentation, and file specifications are available at: https: phac-nml.github.io quasitools Contact gary.vandomselaar@canada.ca		quasitools	Virology Small molecules Sequencing	10.1101/733238		Apache-2.0		12 tools Tool Name Description Consensus Sequence 0.7.0+galaxy1 Consensus Sequence: Generate a consensus sequence from a BAM file Complexity BAM 0.7.0+galaxy1 Complexity BAM: Quasispecies Distance 0.7.0+galaxy1 Quasispecies Distance: Calculate the evolutionary distance between viral quasispecies. Complexity FASTA 0.7.0+galaxy1 Complexity FASTA: Nucleotide Variants 0.7.0+galaxy1 Nucleotide Variants: Identifies nucleotide variants Quality control 0.7.0+galaxy1 Quality control: Performs quality control on FASTQ reads. Amino Acid Variants 0.7.0+galaxy1 Amino Acid Variants: Identifies amino acid mutations Hydra pipeline 0.7.0+galaxy1 Hydra pipeline: Identifies drug resistance within an NGS dataset Codon Variants 0.7.0+galaxy1 Codon Variants: Identifies codon variants and non-synonymous/synonymous mutations dNdS Report 0.7.0+galaxy1 dNdS Report: Calculate the dN/dS value for each region in a bed file Amino Acid Coverage 0.7.0+galaxy1 Amino Acid Coverage: Builds an aa census and returns its coverage Drug Resistance Mutations 0.7.0+galaxy1 Drug Resistance Mutations:
QUAST	QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.		quast	Sequence assembly	QUAST: Quality assessment tool for genome assemblies		GPL-2.0		Quast 5.2.0+galaxy1		5.1.0rc15.2.0 5.1.0rc15.2.0		5.0.2-foss-2021a5.2.0-foss-2022a (D) 5.0.2-foss-2021a5.2.0-foss-2022a (D)
query_tabular	Query Tabular is a Galaxy-based tool which manipulates tabular files. Query Tabular automatically creates a SQLite database directly from a tabular file within a Galaxy workflow. The SQLite database can be saved to the Galaxy history, and further process to generate tabular outputs containing desired information and formatting.		query_tabular	Bioinformatics Workflows	Improve your Galaxy text life: The Query Tabular Tool		CC-BY-4.0		Query Tabular 3.3.2
R	Free software environment for statistical computing and graphics.		r	Mathematics Data architecture, analysis and design Statistics and probability	10.11120/msor.2001.01010023					3.6.1 4.0.0 4.1.0 4.2.1			4.1.0-foss-2021a4.2.1-foss-2021a4.2.1-foss-2022a (D) 4.1.0-foss-2021a4.2.1-foss-2021a4.2.1-foss-2022a (D) 4.1.0-foss-2021a4.2.1-foss-2021a4.2.1-foss-2022a (D)
r-raceid			r-raceid						5 tools Tool Name Description Lineage computation using StemID 3.1 Lineage computation using StemID: generates lineage from prior clustering Initial processing using RaceID 3.1 Initial processing using RaceID: performs filtering, normalisation, and confounder removal to generate a normalised and filtered count matrix of single-cell RNA data Clustering using RaceID 3.1 Clustering using RaceID: performs clustering, outlier detection, dimensional reduction Lineage Branch Analysis using StemID 3.1 Lineage Branch Analysis using StemID: inspects branches of a lineage tree Cluster Inspection using RaceID 3.1 Cluster Inspection using RaceID: examines gene expression within clusters
Racon	Consensus module for raw de novo DNA assembly of long uncorrected reads Racon 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.		racon	Whole genome sequencing Sequence assembly	Constructing a reference genome in a single lab: The possibility to use oxford nanopore technology		MIT		Racon 1.5.0+galaxy1		1.4.3
RaGOO	fast and accurate reference-guided scaffolding of draft genomes. Fast Reference-Guided Scaffolding of Genome Assembly Contigs. Index of /shares/schatzlab/www-data/ragoo. A tool to order and orient genome assembly contigs via Minimap2 alignments to a reference genome. Alonge, Michael, et al. "RaGOO: fast and accurate reference-guided scaffolding of draft genomes." Genome biology 20.1 (2019): 1-17. Contigs and reference fasta files may now be gzipped. RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:		ragoo	Sequence assembly Sequencing Plant biology Cell biology	RaGOO: Fast and accurate reference-guided scaffolding of draft genomes		MIT		RaGOO 1.0
ragtag	RagTag is a collection of software tools for scaffolding and improving modern genome assemblies.		ragtag	Sequence assembly	RaGOO: Fast and accurate reference-guided scaffolding of draft genomes		MIT		RagTag 2.1.0+galaxy1
RAMClustR	A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.		ramclustr	Metabolomics	RAMClust: A novel feature clustering method enables spectral-matching-based annotation for metabolomics data		GPL-2.0		2 tools Tool Name Description RAMClustR define experiment 1.0.2+galaxy2 RAMClustR define experiment: Definition of experimental design used for record keeping and writing spectra data. RAMClustR 1.3.0+galaxy7 RAMClustR: A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.
Ratatosk	Ratatosk – Hybrid error correction of long reads enables accurate variant calling and assembly. Phased hybrid error correction of long reads using colored de Bruijn graphs. Ratatosk is a phased error correction tool for erroneous long reads based on compacted and colored de Bruijn graphs built from accurate short reads.		ratatosk	DNA polymorphism Sequence assembly Whole genome sequencing	10.1101/2020.07.15.204925		BSD-2-Clause						0.7.6.3--h43eeafb_2
raven	a de novo genome assembler for long reads. Raven is a de novo genome assembler for long uncorrected reads.		raven	Sequence assembly Whole genome sequencing Genomics	10.1101/2020.08.07.242461		MIT		Raven 1.8.3+galaxy0
Raw Tools	A standalone tool for extracting data directly from raw files generated by Thermo Orbitrap family instruments.		rawtools	Proteomics experiment Proteomics	RawTools: Rapid and Dynamic Interrogation of Orbitrap Data Files for Mass Spectrometer System Management		Apache-2.0		Raw Tools 1.4.2.0
RAxML	A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.		raxml	Phylogenetics Sequence analysis	2 publications Publications 10.1093/bioinformatics/btu033 10.1093/bioinformatics/btl446	RAxML			RAxML 8.2.12+galaxy1				8.2.12
rdkit	RDKit is an Open-Source Cheminformatics Software. Fast, Efficient Fragment-Based Coordinate Generation for Open Babel.		rdkit	Cheminformatics Medicinal chemistry Molecular biology	10.26434/CHEMRXIV.7791947.V2				2 tools Tool Name Description Enumerate changes 2020.03.4+galaxy0 Enumerate changes: calculated with Dimorphite DL and RDKit Max SuCOS score 2020.03.4+galaxy0 Max SuCOS score: - determine maximum SuCOS score of ligands against clustered fragment hits
rdock			rdock						Create Frankenstein ligand 2013.1-0+galaxy0
recetox-aplcms	recetox-aplcms is a tool for peak detection in mass spectrometry data. The tool performs (1) noise removal, (2) peak detection, (3) retention time drift correction, (4) peak alignment and (5) weaker signal recovery as well as (6) suspect screening.		recetox-aplcms	Metabolomics			GPL-2.0		8 tools Tool Name Description recetox-aplcms - remove noise 0.13.2+galaxy0 recetox-aplcms - remove noise: filter noise and detect peaks in high resolution mass spectrometry (HRMS) profile data recetox-aplcms - merge known table 0.13.2+galaxy0 recetox-aplcms - merge known table: join knowledge from aligned features and known table. recetox-aplcms - generate feature table 0.13.2+galaxy0 recetox-aplcms - generate feature table: generate feature table from noise-removed HRMS profile data recetox-aplcms - correct time 0.13.2+galaxy0 recetox-aplcms - correct time: correct retention time across samples for peak alignment recetox-aplcms - compute clusters 0.13.2+galaxy0 recetox-aplcms - compute clusters: compute clusters of mz and rt across samples and assign cluster IDs to individual features recetox-aplcms - align features 0.13.2+galaxy0 recetox-aplcms - align features: align peaks across samples recetox-aplcms - compute template 0.13.2+galaxy0 recetox-aplcms - compute template: compute retention time correction template feature table recetox-aplcms - recover weaker signals 0.13.2+galaxy0 recetox-aplcms - recover weaker signals: recover weaker signals from raw data using an aligned feature table
recon	Tool for calculating the probability of nucleosome formation along a DNA sequence input by the user.		recon	DNA DNA binding sites Statistics and probability DNA packaging Transcription factors and regulatory sites	RECON: A program for prediction of nucleosome formation potential						1.08
RED	This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data.		red	RNA Sequencing Data visualisation	RED: A Java-MySQL software for identifying and visualizing RNA editing sites using rule- based and statistical filters				Red 2018.09.10+galaxy1
regenie			regenie										3.2.9
RepeatMasker	A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).		repeatmasker	Sequence analysis Sequence composition, complexity and repeats			OSL-2.1		RepeatMasker 4.1.5+galaxy0		4.1.2-p14.1.5 4.1.2-p14.1.5		4.1.5--pl5321hdfd78af_0
RepeatModeler2	RepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data.		repeatmodeler	Model organisms Sequence composition, complexity and repeats Whole genome sequencing Sequence assembly Mobile genetic elements	10.1101/856591				RepeatModeler 2.0.4+galaxy1		2.0.32.0.42.0.4-conda 2.0.32.0.42.0.4-conda 2.0.32.0.42.0.4-conda		2.0.4--pl5321hdfd78af_0
RepeatScout	RepeatScout is a tool to discover repetitive substrings in DNA.		repeatscout	DNA	10.1093/bioinformatics/bti1018						1.0.6
RepEnrich			repenrich						RepEnrich 1.6.1
rjags	The rjags package provides an interface from R to the JAGS library for Bayesian data analysis. JAGS uses Markov Chain Monte Carlo (MCMC) to generate a sequence of dependent samples from the posterior distribution of the parameters.		rjags	Statistics and probability			GPL-2.0						4-10-foss-2021a-r-4.1.0
RMassBank	Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.		rmassbank	Metabolomics	Automatic recalibration and processing of tandem mass spectra using formula annotation		Artistic-2.0		RMassBank 3.0.0+galaxy3
rmats-turbo			rmats-turbo										4.1.2
rmblast	RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler.		rmblast	Genomics			OSL-2.1				2.11.02.14.0 2.11.02.14.0
rnachipintegrator			rnachipintegrator						2 tools Tool Name Description Analyse canonical genes against 'peak' data 1.1.0.0 Analyse canonical genes against 'peak' data: using RnaChipIntegrator RnaChipIntegrator 1.1.0.0 RnaChipIntegrator: Integrated analysis of 'gene' and 'peak' data
rnaQUAST	Quality assessment tool for de novo transcriptome assemblies.		rnaquast	Sequence assembly Transcriptomics RNA-seq	RnaQUAST: A quality assessment tool for de novo transcriptome assemblies		Unlicense		rnaQUAST 2.2.3+galaxy0
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.		roary	DNA Genomics Mapping	10.1093/bioinformatics/btv421	roary			Roary 3.13.0+galaxy3
RSEM	We present a generative statistical model and associated inference methods that handle read mapping uncertainty in a principled manner. Through simulations parameterized by real RNASeq data, we show that our method is more accurate than previous methods. Our improved accuracy is the result of handling read mapping uncertainty with a statistical model and the estimation of gene expression levels as the sum of isoform expression levels.		rsem	RNA-Seq	RNA-Seq gene expression estimation with read mapping uncertainty	RSEM							1.3.3--pl5321ha04fe3b_5
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.		rseqc	Sequencing	2 publications Publications RSeQC: Quality control of RNA-seq experiments Measure transcript integrity using RNA-seq data	rseqc			22 tools Tool Name Description Gene Body Coverage (Bigwig) 5.0.1+galaxy2 Gene Body Coverage (Bigwig): read coverage over gene body Read GC 5.0.1+galaxy2 Read GC: determines GC% and read count Read Quality 5.0.1+galaxy2 Read Quality: determines Phred quality score Transcript Integrity Number 5.0.1+galaxy2 Transcript Integrity Number: evaluates RNA integrity at a transcript level Deletion Profile 5.0.1+galaxy2 Deletion Profile: calculates the distributions of deleted nucleotides across reads Read Distribution 5.0.1+galaxy2 Read Distribution: calculates how mapped reads were distributed over genome feature FPKM Count 5.0.1+galaxy2 FPKM Count: calculates raw read count, FPM, and FPKM for each gene Junction Annotation 5.0.1+galaxy2 Junction Annotation: compares detected splice junctions to reference gene model RNA fragment size 5.0.1+galaxy2 RNA fragment size: calculates the fragment size for each gene/transcript Insertion Profile 5.0.1+galaxy2 Insertion Profile: calculates the distribution of inserted nucleotides across reads RPKM Saturation 5.0.1+galaxy2 RPKM Saturation: calculates raw count and RPKM values for transcript at exon, intron, and mRNA level Read Duplication 5.0.1+galaxy2 Read Duplication: determines reads duplication rate with sequence-based and mapping-based strategies Gene Body Coverage (BAM) 5.0.1+galaxy2 Gene Body Coverage (BAM): read coverage over gene body BAM/SAM Mapping Stats 5.0.1+galaxy2 BAM/SAM Mapping Stats: reads mapping statistics for a provided BAM or SAM file. BAM to Wiggle 5.0.1+galaxy2 BAM to Wiggle: converts all types of RNA-seq data from .bam to .wig Junction Saturation 5.0.1+galaxy2 Junction Saturation: detects splice junctions from each subset and compares them to reference gene model Infer Experiment 5.0.1+galaxy2 Infer Experiment: speculates how RNA-seq were configured Mismatch Profile 5.0.1+galaxy2 Mismatch Profile: calculates the distribution of mismatches across reads Hexamer frequency 5.0.1+galaxy2 Hexamer frequency: calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences Clipping Profile 5.0.1+galaxy2 Clipping Profile: estimates clipping profile of RNA-seq reads from BAM or SAM file Read NVC 5.0.1+galaxy2 Read NVC: to check the nucleotide composition bias Inner Distance 5.0.1+galaxy2 Inner Distance: calculate the inner distance (or insert size) between two paired RNA reads		5.0.1
Rstudio	Integrated development environment (IDE) for the R programming language.		rstudio	Mathematics Data architecture, analysis and design Statistics and probability	RSTUDIO: A platform-independent IDE for R and sweave				RStudio 0.3
rtg-tools	RTG Core: Software for alignment and analysis of next-gen sequencing data.		rtg-tools	Genomics			Other				3.12.1
rxdock			rxdock						2 tools Tool Name Description rxDock cavity definition 2013.1.1_148c5bd1+galaxy0 rxDock cavity definition: - generate the active site definition needed for rxDock docking rxDock docking 2013.1.1_148c5bd1+galaxy0 rxDock docking: - perform protein-ligand docking with rxDock
s3segmenter			s3segmenter						s3segmenter 1.3.12+galaxy0
sailfish	A software tool that implements a novel, is an alignment-free algorithm for the estimation of isoform abundances directly from a set of reference sequences and RNA-seq reads.		sailfish	RNA-Seq RNA Sequencing Transcriptomics	Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms				Sailfish 0.10.1.1
Salmon	A tool for transcript expression quantification from RNA-seq data		salmon	RNA-Seq Gene expression Transcriptomics	Salmon provides fast and bias-aware quantification of transcript expression		GPL-3.0		Salmon quant 1.10.1+galaxy2	1.1.0			1.4.0-gompi-2021a1.9.0-gcc-11.3.0 (D) 1.4.0-gompi-2021a1.9.0-gcc-11.3.0 (D)
salmonKallistoMtxTo10x			salmon_kallisto_mtx_to_10x						salmonKallistoMtxTo10x 0.0.1+galaxy6
salsa	> VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch		salsa	Sequence assembly DNA binding sites Mapping	Integrating Hi-C links with assembly graphs for chromosome-scale assembly		MIT						2.3
sam2interval			sam2interval						Convert SAM 1.0.2
sam_pileup			sam_pileup						Generate pileup 1.1.3
sambamba	This tool is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM formats.		sambamba	DNA Sequence analysis RNA-Seq	Sambamba: Fast processing of NGS alignment formats				Sample, Slice or Filter BAM 0.7.1+galaxy1	0.8.1		0.8.1--h41abebc_0
samblaster	A tool to mark duplicates and extract discordant and split reads from SAM files.		samblaster	DNA Sequencing Mapping	SAMBLASTER: Fast duplicate marking and structural variant read extraction	samblaster				0.1.24
SAMTools	SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.		samtools	Mapping Sequence analysis Sequencing Rare diseases	3 publications Publications The Sequence Alignment/Map format and SAMtools Twelve years of SAMtools and BCFtools A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data	SAMTools	MIT		23 tools Tool Name Description Samtools markdup 1.15.1+galaxy2 Samtools markdup: marks duplicate alignments Samtools coverage 1.15.1+galaxy2 Samtools coverage: computes the depth at each position or region Samtools split 1.15.1+galaxy2 Samtools split: BAM dataset on readgroups Samtools fastx 1.15.1+galaxy2 Samtools fastx: extract FASTA or FASTQ from alignment files Samtools calmd 2.0.4 Samtools calmd: recalculate MD/NM tags Samtools stats 2.0.5 Samtools stats: generate statistics for BAM dataset Slice 2.0.3 Slice: BAM by genomic regions Samtools reheader 2.0.3 Samtools reheader: copy SAM/BAM header between datasets Samtools mpileup 2.1.7 Samtools mpileup: multi-way pileup of variants Samtools idxstats 2.0.5 Samtools idxstats: reports stats of the BAM index file Samtools bedcov 2.0.4 Samtools bedcov: calculate read depth for a set of genomic intervals BAM-to-SAM 2.0.4 BAM-to-SAM: convert BAM to SAM SAM-to-BAM 2.1.2 SAM-to-BAM: convert SAM to BAM Filter SAM or BAM, output SAM or BAM 1.8+galaxy1 Filter SAM or BAM, output SAM or BAM: files on FLAG MAPQ RG LN or by region Samtools flagstat 2.0.5 Samtools flagstat: tabulate descriptive stats for BAM datset Samtools merge 1.15.1+galaxy2 Samtools merge: merge multiple sorted alignment files Samtools phase 2.0.2 Samtools phase: call and phase heterozygous SNPs RmDup 2.0.1 RmDup: remove PCR duplicates Samtools sort 2.0.5 Samtools sort: order of storing aligned sequences Samtools view 1.15.1+galaxy2 Samtools view: - reformat, filter, or subsample SAM, BAM or CRAM Samtools depth 1.15.1+galaxy2 Samtools depth: compute the depth at each position or region Samtools fixmate 1.15.1+galaxy2 Samtools fixmate: fill mate coordinates, ISIZE and mate related flags samtools BAM to CRAM 1.15.1+galaxy2 samtools BAM to CRAM: convert BAM alignments to CRAM format	1.9 1.10 1.12	1.181.19.2 1.181.19.2	1.15--h3843a85_0	1.13-gcc-10.3.01.13-gcc-11.3.01.16.1-gcc-11.3.0 (D) 1.13-gcc-10.3.01.13-gcc-11.3.01.16.1-gcc-11.3.0 (D) 1.13-gcc-10.3.01.13-gcc-11.3.01.16.1-gcc-11.3.0 (D)
scanpy	Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.		scanpy	Gene expression Cell biology Genetics	SCANPY: Large-scale single-cell gene expression data analysis		BSD-3-Clause		34 tools Tool Name Description Filter 1.9.6+galaxy4 Filter: with scanpy Plot 1.9.6+galaxy4 Plot: with scanpy Cluster, infer trajectories and embed 1.9.6+galaxy4 Cluster, infer trajectories and embed: with scanpy Remove confounders 1.9.6+galaxy4 Remove confounders: with scanpy Normalize 1.9.6+galaxy4 Normalize: and impute with scanpy Inspect and manipulate 1.9.6+galaxy4 Inspect and manipulate: with scanpy AnnData Operations 1.8.1+galaxy93 AnnData Operations: modifies metadata and flags genes Scanpy FilterGenes 1.9.3+galaxy0 Scanpy FilterGenes: based on counts and numbers of cells expressed Scanpy ScaleData 1.9.3+galaxy0 Scanpy ScaleData: to make expression variance the same for all genes Scanpy RunUMAP 1.9.3+galaxy0 Scanpy RunUMAP: visualise cell clusters using UMAP Scanpy RunTSNE 1.9.3+galaxy0 Scanpy RunTSNE: visualise cell clusters using tSNE Scanpy RunPCA 1.9.3+galaxy0 Scanpy RunPCA: for dimensionality reduction Scanpy PAGA 1.9.3+galaxy0 Scanpy PAGA: trajectory inference Scanpy RunFDG 1.9.3+galaxy0 Scanpy RunFDG: visualise cell clusters using force-directed graph Scanpy DPT 1.9.3+galaxy0 Scanpy DPT: diffusion pseudotime inference Scanpy DiffusionMap 1.9.3+galaxy0 Scanpy DiffusionMap: calculate diffusion components Scanpy Read10x 1.9.3+galaxy0 Scanpy Read10x: into hdf5 object handled by scanpy Scanpy PlotTrajectory 1.9.3+galaxy0 Scanpy PlotTrajectory: visualise cell trajectories Scanpy PlotEmbed 1.9.3+galaxy0 Scanpy PlotEmbed: visualise cell embeddings Scanpy ParameterIterator 0.0.1+galaxy9 Scanpy ParameterIterator: produce an iteration over a defined parameter Scanpy NormaliseData 1.9.3+galaxy0 Scanpy NormaliseData: to make all cells having the same total expression Scanpy MNN 1.9.3+galaxy0 Scanpy MNN: correct batch effects by matching mutual nearest neighbors Scanpy ComBat 1.9.3+galaxy0 Scanpy ComBat: adjust expression for variables that might introduce batch effect Scanpy FindVariableGenes 1.9.3+galaxy1 Scanpy FindVariableGenes: based on normalised dispersion of expression Scanpy FindMarkers 1.9.3+galaxy0 Scanpy FindMarkers: to find differentially expressed genes between groups Scanpy FindCluster 1.9.3+galaxy0 Scanpy FindCluster: based on community detection on KNN graph Scanpy FilterCells 1.9.3+galaxy0 Scanpy FilterCells: based on counts and numbers of genes expressed AnnData Operations 1.9.3+galaxy0 AnnData Operations: is a Swiss army knife for AnnData files Scanpy ComputeGraph 1.9.3+galaxy0 Scanpy ComputeGraph: to derive kNN graph Scanpy BBKNN 1.9.3+galaxy0 Scanpy BBKNN: batch-balanced K-nearest neighbours Scanpy Harmony 1.9.3+galaxy0 Scanpy Harmony: adjust principal components for variables that might introduce batch effect Scanpy Scrublet 1.9.3+galaxy0 Scanpy Scrublet: remove multiplets from annData objects with Scrublet Scanpy Plot Scrublet 1.9.3+galaxy0 Scanpy Plot Scrublet: visualise multiplet scoring distribution Scanpy RegressOut 1.9.3+galaxy0 Scanpy RegressOut: variables that might introduce batch effect
scater	Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data.		scater	RNA-seq Quality affairs Molecular genetics	Scater: Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R				6 tools Tool Name Description Scater: t-SNE plot 1.22.0 Scater: t-SNE plot: of two components Scater: plot expression frequency 1.12.2 Scater: plot expression frequency: Plot the frequency of expression against the mean expression level for SCE Scater: calculate QC metrics 1.22.0 Scater: calculate QC metrics: from single-cell expression matrix Scater: filter SCE 1.22.0 Scater: filter SCE: with user-defined parameters or PCA Scater: plot library QC 1.22.0 Scater: plot library QC: to visualise library size, feature counts and mito gene expression Scater: PCA plot 1.22.0 Scater: PCA plot: cell-level reduced dimension of a normalised SCE
scikit-build			scikit-build										0.11.1-gcccore-10.3.0
scikit-image	Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc.		scikit-image	Imaging Software engineering Literature and language	10.7287/PEERJ.PREPRINTS.336V2		BSD-3-Clause		7 tools Tool Name Description Filter 2-D image 1.12.0+galaxy1 Filter 2-D image: with scipy Filter label map by rules 0.0.1-4 Filter label map by rules: Threshold image 0.18.1+galaxy3 Threshold image: with scikit-image Extract image features 0.18.1+galaxy0 Extract image features: with scikit-image Count objects in label map 0.0.5-2 Count objects in label map: Perform histogram equalization 0.18.1+galaxy0 Perform histogram equalization: with scikit-image Convert binary image to label map 0.5+galaxy0 Convert binary image to label map:
Scikit-learn			scikit						14 tools Tool Name Description Estimator attributes 1.0.11.0 Estimator attributes: get important attributes from an estimator or scikit object Pipeline Builder 1.0.11.0 Pipeline Builder: an all-in-one platform to build pipeline, single estimator, preprocessor and custom wrappers Numeric Clustering 1.0.11.0 Numeric Clustering: Nearest Neighbors Classification 1.0.11.0 Nearest Neighbors Classification: Machine Learning Visualization Extension 1.0.11.0 Machine Learning Visualization Extension: includes several types of plotting for machine learning Create a deep learning model architecture 1.0.11.0 Create a deep learning model architecture: using Keras Ensemble methods 1.0.11.0 Ensemble methods: for classification and regression To categorical 1.0.11.0 To categorical: Converts a class vector (integers) to binary class matrix Support vector machines (SVMs) 1.0.11.0 Support vector machines (SVMs): for classification Hyperparameter Search 1.0.11.0 Hyperparameter Search: performs hyperparameter optimization using various SearchCVs Create deep learning model 1.0.11.0 Create deep learning model: with an optimizer, loss function and fit parameters Deep learning training and evaluation 1.0.11.0 Deep learning training and evaluation: conduct deep training and evaluation either implicitly or explicitly Model Prediction 1.0.11.0 Model Prediction: predicts on new data using a preffited model Generalized linear models 1.0.11.0 Generalized linear models: for classification and regression
scipio			scipio								1.4
send_to_cloud			send_to_cloud						Send to cloud 0.1.0
sepp	SEPP stands for SATé-Enabled Phylogenetic Placement and addresses the problem of phylogenetic placement for meta-genomic short reads		sepp	Phylogenetics	10.1142/9789814366496_0024	sepp	GPL-3.0				4.5.1		4.5.0-foss-2021a4.5.1-foss-2022a (D) 4.5.0-foss-2021a4.5.1-foss-2022a (D)
seq_select_by_id			seq_select_by_id						Select sequences by ID 0.0.14
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.		seqkit	Database management Sequence analysis	10.1371/journal.pone.0163962				2 tools Tool Name Description SeqKit sort 2.8.1+galaxy0 SeqKit sort: FASTA or FASTQ files SeqKit statistics 2.8.1+galaxy0 SeqKit statistics: of FASTA/Q files		2.2.02.3.12.5.1 2.2.02.3.12.5.1 2.2.02.3.12.5.1
seqlib			seqlib										1.2.0-gcc-10.3.0
seqtk	A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip.		seqtk	Data management	FastQ-brew: Module for analysis, preprocessing, and reformatting of FASTQ sequence data	seqtk	MIT		15 tools Tool Name Description seqtk_telo 1.4+galaxy0 seqtk_telo: find telomeres seqtk_mutfa 1.4+galaxy0 seqtk_mutfa: point mutate FASTA at specified positions seqtk_subseq 1.4+galaxy0 seqtk_subseq: extract subsequences from FASTA/Q files seqtk_cutN 1.4+galaxy0 seqtk_cutN: cut sequence at long N seqtk_listhet 1.4+galaxy0 seqtk_listhet: extract the position of each het seqtk_mergepe 1.4+galaxy0 seqtk_mergepe: interleave two unpaired FASTA/Q files for a paired-end file seqtk_seq 1.4+galaxy0 seqtk_seq: common transformation of FASTA/Q seqtk_mergefa 1.4+galaxy0 seqtk_mergefa: merge two FASTA/Q files seqtk_sample 1.4+galaxy0 seqtk_sample: random subsample of fasta or fastq sequences seqtk_dropse 1.4+galaxy0 seqtk_dropse: drop unpaired from interleaved Paired End FASTA/Q seqtk_fqchk 1.4+galaxy0 seqtk_fqchk: fastq QC (base/quality summary) seqtk_trimfq 1.4+galaxy0 seqtk_trimfq: trim FASTQ using the Phred algorithm seqtk_randbase 1.4+galaxy0 seqtk_randbase: choose a random base from hets seqtk_hety 1.4+galaxy0 seqtk_hety: regional heterozygosity seqtk_comp 1.4+galaxy0 seqtk_comp: get the nucleotide composition of FASTA/Q	1.3	1.4		1.3-gcc-10.3.01.3-gcc-11.3.0 (D) 1.3-gcc-10.3.01.3-gcc-11.3.0 (D)
seurat	Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.		seurat	RNA-Seq Transcriptomics	Integrated analysis of multimodal single-cell data		MIT		16 tools Tool Name Description Seurat 4.3.0.1+galaxy1 Seurat: - toolkit for exploration of single-cell RNA-seq data Seurat ScaleData 4.0.4+galaxy0 Seurat ScaleData: scale and center genes Seurat RunTSNE 4.0.4+galaxy0 Seurat RunTSNE: run t-SNE dimensionality reduction Seurat RunPCA 4.0.4+galaxy0 Seurat RunPCA: run a PCA dimensionality reduction Seurat Read10x 4.0.4+galaxy0 Seurat Read10x: Loads Tabular or 10x data into a serialized seurat R object Plot 4.0.4+galaxy0 Plot: with Seurat Seurat FindVariableGenes 4.0.4+galaxy0 Seurat FindVariableGenes: identify variable genes Seurat FindNeighbours 4.0.4+galaxy0 Seurat FindNeighbours: constructs a Shared Nearest Neighbor (SNN) Graph Seurat FindMarkers 4.0.4+galaxy0 Seurat FindMarkers: find markers (differentially expressed genes) Seurat FilterCells 4.0.4+galaxy0 Seurat FilterCells: filter cells in a Seurat object Seurat Export2CellBrowser 4.0.4+galaxy0 Seurat Export2CellBrowser: produces files for UCSC CellBrowser import. Seurat CreateSeuratObject 2.3.1+galaxy0 Seurat CreateSeuratObject: create a Seurat object Seurat Plot dimension reduction 4.0.4+galaxy0 Seurat Plot dimension reduction: graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class. Seurat FindClusters 4.0.4+galaxy0 Seurat FindClusters: find clusters of cells Seurat NormaliseData 4.0.4+galaxy0 Seurat NormaliseData: normalise data Seurat UMAP 4.0.4+galaxy0 Seurat UMAP: dimensionality reduction
shasta	De novo assembly from Oxford Nanopore reads.		shasta	Genomics Sequence assembly	Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes		MIT		Shasta 0.6.0+galaxy0
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.		shovill	Genomics Microbiology Sequence assembly		shovill	GPL-3.0		Shovill 1.1.0+galaxy2				1.1.0
sicer	A clustering approach for identification of enriched domains from histone modification ChIP-seq data.		sicer	ChIP-seq Epigenomics	A clustering approach for identification of enriched domains from histone modification ChIP-Seq data				SICER 1.1
SimText	A text mining framework for interactive analysis and visualization of similarities among biomedical entities. For each search query, PMIDs or abstracts from PubMed are saved. $ git clone https://github.com/dlal-group/simtext. For all PMIDs in each row of a table the according abstracts are saved in additional columns.		simtext	Natural language processing Workflows Machine learning Molecular interactions, pathways and networks	10.1101/2020.07.06.190629				2 tools Tool Name Description PMIDs to PubTator 0.0.2 PMIDs to PubTator: binary matrix PubMed query 0.0.2 PubMed query: download a defined number of abstracts or PMIDs from PubMed
SIP			sip								6.7.9
sistr	The Salmonella In Silico Typing Resource (SISTR) is an open-source and freely available web application for rapid in silico typing and serovar prediction from Salmonella genome assemblies using cgMLST and O and H antigen gene searching.		sistr	Whole genome sequencing Immunoproteins and antigens Sequence assembly Zoology Public health and epidemiology	Performance and accuracy of four open-source tools for in silico serotyping of salmonella spp. Based on whole-genome short-read sequencing data		Apache-2.0		sistr_cmd 1.1.1+galaxy1
slow5-dorado			slow5-dorado								0.2.1
slow5-guppy			slow5-guppy								6.0.1
slow5tools	Slow5tools is a simple toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. About SLOW5 format: SLOW5 is a new file format for storing signal data from Oxford Nanopore Technologies (ONT) devices. SLOW5 was developed to overcome inherent limitations in the standard FAST5 signal data format that prevent efficient, scalable analysis and cause many headaches for developers. SLOW5 can be encoded in human-readable ASCII format, or a more compact and efficient binary format (BLOW5) - this is analogous to the seminal SAM/BAM format for storing DNA sequence alignments. The BLOW5 binary format supports zlib (DEFLATE) compression, or other compression methods, thereby minimising the data storage footprint while still permitting efficient parallel access. Detailed benchmarking experiments have shown that SLOW5 format is an order of magnitude faster and significantly smaller than FAST5.		slow5tools							0.8.0	0.3.01.0.01.1.0 0.3.01.0.01.1.0 0.3.01.0.01.1.0
smithwaterman			smithwaterman										20160702-gcccore-10.3.0
Smudgeplots	Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568		Smudgeplots	Sequence assembly Genetic variation Mathematics	10.1101/747568		Apache-2.0		Smudgeplot 0.2.5+galaxy3
Snakemake	Workflow engine and language. It aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style.		snakemake	Bioinformatics Workflows Software engineering	Snakemake-a scalable bioinformatics workflow engine	Snakemake					7.18.2		6.6.1-foss-2021a7.22.0-foss-2022a (D) 6.6.1-foss-2021a7.22.0-foss-2022a (D)
SNAP	The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool.		snap	DNA DNA polymorphism Genetics	10.1186/1471-2105-5-59	SNAP			Train SNAP 2013_11_29+galaxy1		2006		2013_11_29
SnapATAC	SnapATAC (Single Nucleus Analysis Pipeline for ATAC-seq) is a fast, accurate and comprehensive method for analyzing single cell ATAC-seq datasets.		snapatac	Epigenomics Cell biology Chromosome conformation capture Mapping Sequencing	Comprehensive analysis of single cell ATAC-seq data with SnapATAC		GPL-3.0		4 tools Tool Name Description SnapATAC2 Preprocessing 2.6.4+galaxy1 SnapATAC2 Preprocessing: and integration SnapATAC2 peaks and motif 2.6.4+galaxy1 SnapATAC2 peaks and motif: analysis SnapATAC2 Clustering 2.6.4+galaxy1 SnapATAC2 Clustering: and dimension reduction SnapATAC2 Plotting 2.6.4+galaxy1 SnapATAC2 Plotting:
SNAPPy	a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing | SNAPPy is a Snakemake pipeline for HIV-1 subtyping by phylogenetic pairing | This is the repository for SNAPPy, a Snakemake pipeline for HIV-1 subtyping by phylogenetic pairing. SNAPPy allows high-throughput HIV-1 subtyping locally while being resource efficient and scalable. This pipeline was constructed using Snakemake , and it uses MAFFT and for multiple sequence alignment, BLAST for similarirty querys, IQ-TREE for phylogenetic inference, and several Biopython modules for data parsing an analysis. For in-depth information on how the tool works please visit the documentation page. SNAPPy was design for Linux based operative systems | Welcome to snappy’s documentation! — SNAPPy-HIV1-Subtyping 1.0.0 documentation | Free document hosting provided by Read the Docs		snappy	Phylogenetics Workflows Public health and epidemiology	SNAPPy: A snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing		MIT						1.1.8-gcccore-10.3.01.1.9-gcccore-11.3.0 (D) 1.1.8-gcccore-10.3.01.1.9-gcccore-11.3.0 (D)
sniffles	An algorithm for structural variation detection from third generation sequencing alignment.		sniffles	DNA structural variation Sequencing	Accurate detection of complex structural variations using single-molecule sequencing	sniffles	MIT		sniffles 1.0.12+galaxy0		2.0.22.3.32.4 2.0.22.3.32.4 2.0.22.3.32.4
snippy	Rapid haploid variant calling and core SNP phylogeny generation.		snippy	Genomics Model organisms DNA polymorphism Phylogenetics		snippy	GPL-3.0		3 tools Tool Name Description snippy-clean_full_aln 4.6.0+galaxy0 snippy-clean_full_aln: Replace any non-standard sequence characters in snippy 'core.full.aln' file. snippy-core 4.6.0+galaxy0 snippy-core: Combine multiple Snippy outputs into a core SNP alignment snippy 4.6.0+galaxy0 snippy: Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
snp-dists			snp-dists						SNP distance matrix 0.8.2+galaxy0
snp_sites			snp_sites						Finds SNP sites 2.5.1+galaxy0
snpeff	Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes).		snpeff	DNA polymorphism Genetic variation Nucleic acid sites, features and motifs	22728672	snpeff			6 tools Tool Name Description SnpEff chromosome-info: 4.3+T.galaxy2 SnpEff chromosome-info:: list chromosome names/lengths SnpEff build: 4.3+T.galaxy6 SnpEff build:: database from Genbank or GFF record SnpEff databases: 4.3+T.galaxy2 SnpEff databases:: list available databases SnpEff download: 4.3+T.galaxy2 SnpEff download:: download a pre-built database SnpEff eff: 4.3+T.galaxy2 SnpEff eff:: annotate variants SnpEff eff: 4.5covid19 SnpEff eff:: annotate variants for SARS-CoV-2
snpfreq			snpfreq						snpFreq 1.0.1
snpfreqplot			snpfreqplot						Variant Frequency Plot 1.0+galaxy3
snpsift	Toolbox that allows you to filter and manipulate annotated vcf files.		snpsift	Data management Data architecture, analysis and design	Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift		LGPL-3.0		8 tools Tool Name Description SnpSift CaseControl 4.3+t.galaxy0 SnpSift CaseControl: Count samples are in 'case' and 'control' groups. SnpSift vcfCheck 4.3+t.galaxy0 SnpSift vcfCheck: basic checks for VCF specification compliance SnpSift Variant Type 4.3+t.galaxy0 SnpSift Variant Type: Annotate with variant type SnpSift Extract Fields 4.3+t.galaxy0 SnpSift Extract Fields: from a VCF file into a tabular file SnpSift Annotate 4.3+t.galaxy1 SnpSift Annotate: SNPs from dbSnp SnpSift Filter 4.3+t.galaxy1 SnpSift Filter: Filter variants using arbitrary expressions SnpSift rmInfo 4.3+t.galaxy0 SnpSift rmInfo: remove INFO field annotations SnpSift Intervals 4.3+t.galaxy0 SnpSift Intervals: Filter variants using intervals
SOAPdenovo2	SOAPdenovo2 is a next generation sequencing reads de novo assembler.		soapdenovo2	Sequence assembly Sequencing Metagenomics	SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler		GPL-3.0			2.41
sortmerna	Sequence analysis tool for filtering, mapping and OTU-picking NGS reads.		sortmerna	Metatranscriptomics Metagenomics	SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data	sortmerna			Filter with SortMeRNA 4.3.6+galaxy0				4.3.6--h9ee0642_0
Space Ranger			spaceranger										2.0.1-gcc-11.3.0
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.		spades	Sequence assembly	2 publications Publications SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing 10.7490/f1000research.1114334.1	SPAdes	GPL-2.0		8 tools Tool Name Description SPAdes 3.15.5+galaxy2 SPAdes: genome assembler for genomes of regular and single-cell projects rnaviralSPAdes 3.15.5+galaxy2 rnaviralSPAdes: de novo assembler for transcriptomes, metatranscriptomes and metaviromes metaviralSPAdes 3.15.5+galaxy2 metaviralSPAdes: extract and assembly viral genomes from metagenomic data metaplasmidSPAdes 3.15.5+galaxy2 metaplasmidSPAdes: extract and assembly plasmids from metagenomic data coronaSPAdes 3.15.5+galaxy2 coronaSPAdes: SARS-CoV-2 de novo genome assembler biosyntheticSPAdes 3.15.5+galaxy2 biosyntheticSPAdes: biosynthetic gene cluster assembly rnaSPAdes 3.15.5+galaxy2 rnaSPAdes: de novo transcriptome assembler plasmidSPAdes 3.15.5+galaxy2 plasmidSPAdes: extract and assembly plasmids from WGS data			3.15.4--h95f258a_0	3.15.3-gcc-10.3.03.15.5-gcc-11.3.0 (D) 3.15.3-gcc-10.3.03.15.5-gcc-11.3.0 (D)
spectra			spectra										1.0.1-gcccore-11.3.0
Spectral Repeat Finder (SRF)	Spectral Repeat Finder (SRF) is a program to find repeats through an analysis of the power spectrum of a given DNA sequence.		srf	Computational biology	Spectral repeat finders (SRF): Identification of repetitive sequences using Fourier transformation						2022.11.22
sqlite			sqlite								3.36
sra-tools	The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.		sra-tools	DNA Genomics Sequencing	Database resources of the National Center for Biotechnology Information.				3 tools Tool Name Description Download and Extract Reads in BAM 3.1.1+galaxy1 Download and Extract Reads in BAM: format from NCBI SRA Faster Download and Extract Reads in FASTQ 3.1.1+galaxy1 Faster Download and Extract Reads in FASTQ: format from NCBI SRA Download and Extract Reads in FASTQ 3.1.1+galaxy1 Download and Extract Reads in FASTQ: format from NCBI SRA		3.0.2		3.0.3-gompi-2022a3.0.3--h87f3376_0 3.0.3-gompi-2022a3.0.3--h87f3376_0
SRST2			srst2										0.2.0--py_4
ssw	A fast implementation of the Smith-Waterman algorithm whose API that can be flexibly used by programs written in C, C++ and other languages.		ssw	Sample collections Genomics Data governance Nucleic acid structure analysis	SSW library: An SIMD Smith-Waterman C/C++ library for use in genomic applications								1.1-gcccore-10.3.0
Stacks	Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis.		stacks	Mapping Population genetics	Stacks: An analysis tool set for population genomics	Stacks	GPL-3.0		25 tools Tool Name Description Stacks2: clone filter 2.55+galaxy4 Stacks2: clone filter: Identify PCR clones Stacks2: cstacks 2.55+galaxy4 Stacks2: cstacks: Generate catalog of loci Stacks2: de novo map 2.55+galaxy4 Stacks2: de novo map: the Stacks pipeline without a reference genome (denovo_map.pl) Stacks2: gstacks 2.55+galaxy4 Stacks2: gstacks: Call variants, genotypes and haplotype Stacks2: kmer filter 2.55+galaxy4 Stacks2: kmer filter: Identify PCR clones Stacks2: populations 2.55+galaxy4 Stacks2: populations: Calculate population-level summary statistics Stacks2: process radtags 2.55+galaxy4 Stacks2: process radtags: the Stacks demultiplexing script Stacks2: reference map 2.55+galaxy4 Stacks2: reference map: the Stacks pipeline with a reference genome (ref_map.pl) Stacks2: process shortreads 2.55+galaxy4 Stacks2: process shortreads: fast cleaning of randomly sheared genomic or transcriptomic data Stacks2: sstacks 2.55+galaxy4 Stacks2: sstacks: Match samples to the catalog Stacks2: tsv2bam 2.55+galaxy4 Stacks2: tsv2bam: Sort reads by RAD locus Stacks2: ustacks 2.55+galaxy4 Stacks2: ustacks: Identify unique stacks Stacks: assemble read pairs by locus 1.46.1 Stacks: assemble read pairs by locus: run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers Stacks: clone filter 1.46.0 Stacks: clone filter: Identify PCR clones Stacks: cstacks 1.46.0 Stacks: cstacks: build a catalogue of loci Stacks: de novo map 1.46.0 Stacks: de novo map: the Stacks pipeline without a reference genome (denovo_map.pl) Stacks: genotypes 1.46.0 Stacks: genotypes: analyse haplotypes or genotypes in a genetic cross ('genotypes' program) Stacks: populations 1.46.3 Stacks: populations: analyze a population of individual samples ('populations' program) Stacks: process radtags 1.46.0 Stacks: process radtags: the Stacks demultiplexing script Stacks: pstacks 1.46.0 Stacks: pstacks: find stacks from short reads mapped to a reference genome Stacks: reference map 1.46.0 Stacks: reference map: the Stacks pipeline with a reference genome (ref_map.pl) Stacks: rxstacks 1.46.0 Stacks: rxstacks: make corrections to genotype and haplotype calls Stacks: sstacks 1.46.1 Stacks: sstacks: match stacks to a catalog Stacks: statistics 1.46.0 Stacks: statistics: on stacks found for multiple samples Stacks: ustacks 1.46.0 Stacks: ustacks: align short reads into stacks
star	Ultrafast universal RNA-seq data aligner		star	RNA-Seq Transcriptomics	3 publications Publications STAR: Ultrafast universal RNA-seq aligner Simulation-based comprehensive benchmarking of RNA-seq aligners Lacking alignments? The next-generation sequencing mapper segemehl revisited	star	GPL-3.0		2 tools Tool Name Description RNA STARSolo 2.7.11a+galaxy0 RNA STARSolo: mapping, demultiplexing and gene quantification for single cell RNA-seq RNA STAR 2.7.11a+galaxy0 RNA STAR: Gapped-read mapper for RNA-seq data		2.7.10a	2.7.10a--h9ee0642_0	2.7.9a-gcc-10.3.02.7.10b-gcc-11.3.0 (D)2.7.10a--h9ee0642_0 2.7.9a-gcc-10.3.02.7.10b-gcc-11.3.0 (D)2.7.10a--h9ee0642_0 2.7.9a-gcc-10.3.02.7.10b-gcc-11.3.0 (D)2.7.10a--h9ee0642_0
STAR-Fusion	STAR-Fusion, a method that is both fast and accurate in identifying fusion transcripts from RNA-Seq data		star_fusion	Gene structure RNA-Seq					STAR-Fusion 0.5.4-3+galaxy1
staramr	staramr (*AMR) scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes. The star|* in staramr indicates that it can handle all of the ResFinder, PointFinder, and PlasmidFinder databases.		staramr	Microbiology Public health and epidemiology Infectious disease					staramr 0.10.0+galaxy1
stringtie	Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.		stringtie	Transcriptomics RNA-seq	StringTie enables improved reconstruction of a transcriptome from RNA-seq reads		Artistic-2.0		2 tools Tool Name Description StringTie 2.2.3+galaxy0 StringTie: transcript assembly and quantification StringTie merge 2.2.3+galaxy0 StringTie merge: transcripts				2.1.7-gcc-10.3.0
subread	Subread is a general-purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. It uses a new mapping paradigm called "seed-and-vote" to achieve fast, accurate and scalable read mapping. It automatically determines if a read should be globally or locally aligned, therefore particularly powerful in mapping RNA-seq reads. It supports indel detection and can map reads with both fixed and variable lengths.		subread	Sequencing Mapping Whole genome sequencing RNA-Seq	2 publications Publications The Subread aligner: Fast, accurate and scalable read mapping by seed-and-vote Simulation-based comprehensive benchmarking of RNA-seq aligners	subread	GPL-3.0				2.0.32.0.6 2.0.32.0.6
SUPER-FOCUS	An agile homology-based approach using a reduced SEED database to report the subsystems present in metagenomic samples and profile their abundances.		superfocus	DNA Metagenomics Sequence analysis	SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data						1.4.1
SUPPA	This tool generates Alternative Splicing (AS) events from an annotation and calculates the PSI ("Percentage Spliced In") value for each event exploiting fast quantification of transcript abundances from multiple samples.		suppa	Transcriptomics RNA splicing	Leveraging transcript quantification for fast computation of alternative splicing profiles		MIT						2.3--py_2
SVIM-asm	Structural variant detection from haploid and diploid genome assemblies. SVIM-asm - Structural variant identification method (Assembly edition). SVIM-asm (pronounced SWIM-assem) is a structural variant caller for haploid or diploid genome-genome alignments. It analyzes a given sorted BAM file (preferably from minimap2) and detects five different variant classes between the query assembly and the reference: deletions, insertions, tandem and interspersed duplications and inversions.		svim-asm	Sequence assembly Genotype and phenotype Sequencing DNA polymorphism	10.1101/2020.10.27.356907		GPL-3.0				1.0.3
SyRI	SyRI is tool for finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.		syri	DNA polymorphism Sequence assembly DNA structural variation Mapping Sequencing	SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies						1.6
TargetFinder	Targetfinder.org provides a web based resource that allows users to find genes that have a similar expression to a query gene signature.		targetfinder	Gene expression Transcription factors and regulatory sites Gene transcripts Small molecules Gene regulation	Targetfinder.org: A resource for systematic discovery of transcription factor target genes				TargetFinder 1.7.0+galaxy1
tb_variant_filter			tb_variant_filter						TB Variant Filter 0.4.0+galaxy0
tbl2asn	Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Genome Workbench but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank.		tbl2asn	Data submission, annotation and curation									20220427-linux6420230119-linux64 (D) 20220427-linux6420230119-linux64 (D)
tbprofiler	A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).		tbprofiler		Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences		GPL-3.0		TB-Profiler Profile 6.2.1+galaxy1
tbvcfreport	The COMBAT-TB Workbench is an IRIDA based, module workbench for M. tuberculosis bioinformatics. It is designed to be easily deployed on a single server.		tbvcfreport	Whole genome sequencing Microbiology Workflows Phylogeny	10.1101/2021.09.23.21263983		Apache-2.0		TB Variant Report 1.0.1+galaxy0
TensorFlow	Prediction of cognitive impairment via deep learning trained with multi-center neuropsychological test data. An end-to-end open source machine learning platform. Announcing the TensorFlow Dev Summit 2020 Learn more. TensorFlow is an end-to-end open source platform for machine learning. It has a comprehensive, flexible ecosystem of tools, libraries and community resources that lets researchers push the state-of-the-art in ML and developers easily build and deploy ML powered applications		tensorflow	Machine learning Pathology Biomarkers	Prediction of cognitive impairment via deep learning trained with multi-center neuropsychological test data					2.0.0 2.1.0 2.3.0 2.4.1 2.6.0 2.8.0
TEsorter	lineage-level classification of transposable elements using conserved protein domains. Note: do not move or hard link TEsorter.py alone to anywhere else, as it rely on database/ and bin/. You can add the directory to PATH or soft link TEsorter.py to PATH		tesorter	Protein folds and structural domains Phylogenetics Transcription factors and regulatory sites Plant biology Model organisms	10.1101/800177						1.4.6
TEtranscripts			TEtranscripts						TEtranscripts 2.2.3+galaxy0
ThermoRawFileParser	Open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and to the HUPO-PSI standard file format mzML		ThermoRawFileParser	Proteomics Proteomics experiment Metabolomics	10.1101/622852		Apache-2.0		Thermo 1.3.4+galaxy0
TMT Analyst			tmt-analyst						TMT Analyst 0.11+galaxy0
tophat	Program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie. A stable SAMtools version is now packaged with the program.		tophat	RNA-Seq Mapping Rare diseases	2 publications Publications TopHat: Discovering splice junctions with RNA-Seq 10.7490/f1000research.1114334.1	tophat			2 tools Tool Name Description TopHat 2.1.1 TopHat: Gapped-read mapper for RNA-seq data Tophat Fusion Post 0.1 Tophat Fusion Post: post-processing to identify fusion genes	2.1.1
TotalView	TotalView is a debugger for High Performance Computing applications.		totalview	Computer science			Proprietary			2019.3.14 2020.1.13
Trans-Proteomic Pipeline (TPP)	Institute for Systems Biology "Trans-Proteomic Pipeline"		tpp	Proteomics Proteomics experiment	4 publications Publications Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics Trans-proteomic pipeline: a pipeline for proteomic analysis. Software pipeline and data analysis for MS/MS proteomics: the trans-proteomic pipeline. A guided tour of the Trans-Proteomic Pipeline				5 tools Tool Name Description Protein Prophet 1.1.1 Protein Prophet: Calculate Protein Prophet statistics on search results PepXML to Table 1.1.1 PepXML to Table: Converts a pepXML file to a tab delimited text file InterProphet 1.1.1 InterProphet: Combine Peptide Prophet results from multiple search engines Peptide Prophet 1.1.1 Peptide Prophet: Calculate Peptide Prophet statistics on search results ProtXML to Table 1.1.1 ProtXML to Table: Converts a ProtXML file to a table
TransDecoder	TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.		transdecoder	Genomics Gene transcripts RNA-Seq Gene expression Sequence assembly Whole genome sequencing					TransDecoder 5.5.0+galaxy2				5.5.0--pl5321hdfd78af_5
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.		transit	DNA Sequencing Mobile genetic elements	TRANSIT - A Software Tool for Himar1 TnSeq Analysis				5 tools Tool Name Description TRANSIT Tn5Gaps 3.0.2+galaxy1 TRANSIT Tn5Gaps: - determine essential genes Convert GFF3 3.0.2+galaxy0 Convert GFF3: to prot_table for TRANSIT TRANSIT Resampling 3.0.2+galaxy1 TRANSIT Resampling: - determine per-gene p-values TRANSIT HMM 3.0.2+galaxy1 TRANSIT HMM: - determine essentiality of a genome TRANSIT Gumbel 3.0.2+galaxy1 TRANSIT Gumbel: - determine essential genes
TransVar			transvar								2.4.0
TreeShrink			treeshrink								1.3.9
trf	Tandem Repeats Finder. Find tandem repeats in DNA sequences without the need to specify either the pattern or pattern size. It uses the method of k-tuple matching to avoid the need for full scale alignment matrix computations. It requires no a priori knowledge of the pattern, pattern size or number of copies. There are no restrictions on the size of the repeats that can be detected. It determines a consensus pattern for the smallest repetitive unit in the tandem repeat.		trf	Sequence analysis Sequence composition, complexity and repeats	Tandem repeats finder: A program to analyze DNA sequences		Other				4.09.1
TRF-mod			trf-mod								4.10.0
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.		trim_galore	Sequence analysis					Trim Galore! 0.6.7+galaxy0
trimAl	Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.		trimal	Sequence analysis Sequencing Sequence sites, features and motifs	trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses						1.4.1
Trimmomatic	A flexible read trimming tool for Illumina NGS data		trimmomatic	Sequencing Sequence analysis Data quality management	RobiNA: A user-friendly, integrated software solution for RNA-Seq-based transcriptomics	Trimmomatic			Trimmomatic 0.36.6		0.39	0.39--hdfd78af_2	0.39-java-11
Trinity / trinityrnaseq	Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads.		trinity	Transcriptomics Gene expression Gene transcripts	2 publications Publications Full-length transcriptome assembly from RNA-Seq data without a reference genome De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis				13 tools Tool Name Description Generate SuperTranscripts 2.15.1+galaxy0 Generate SuperTranscripts: from a Trinity assembly Trinity Stats 2.15.1+galaxy0 Trinity Stats: Describe samples 2.15.1+galaxy0 Describe samples: and replicates Trinity 2.15.1+galaxy1 Trinity: de novo assembly of RNA-Seq data Build expression matrix 2.15.1+galaxy0 Build expression matrix: for a de novo assembly of RNA-Seq data by Trinity Align reads and estimate abundance 2.15.1+galaxy0 Align reads and estimate abundance: on a de novo assembly of RNA-Seq data Extract and cluster differentially expressed transcripts 2.15.1+galaxy0 Extract and cluster differentially expressed transcripts: from a Trinity assembly Compute contig Ex90N50 statistic and Ex90 transcript count 2.15.1+galaxy0 Compute contig Ex90N50 statistic and Ex90 transcript count: from a Trinity assembly Partition genes into expression clusters 2.15.1+galaxy0 Partition genes into expression clusters: after differential expression analysis using a Trinity assembly Filter low expression transcripts 2.15.1+galaxy0 Filter low expression transcripts: from a Trinity assembly Generate gene to transcript map 2.15.1+galaxy0 Generate gene to transcript map: for Trinity assembly Differential expression analysis 2.15.1+galaxy0 Differential expression analysis: using a Trinity assembly RNASeq samples quality check 2.15.1+galaxy0 RNASeq samples quality check: for transcript quantification	2.9.1 2.12.0		2.13.2--ha140323_0	2.9.1-foss-2021a2.15.1--h6ab5fc9_2 2.9.1-foss-2021a2.15.1--h6ab5fc9_2
Trinotate	Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.		trinotate	Gene expression Transcriptomics	A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors				Trinotate 3.2.2+galaxy0				3.2.2--pl5321hdfd78af_1
trnascan-se	A program for improved detection of transfer RNA genes in genomic sequence.		trnascan-se	RNA Genomics Sequence analysis	2 publications Publications tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes 10.1093/nar/25.5.955				tRNA prediction 0.4
Trycycler toolkit	Trycycler: consensus long-read assemblies for bacterial genomes		trycycler	Sequence assembly DNA Human biology Whole genome sequencing Genomics	Trycycler: consensus long-read assemblies for bacterial genomes		GPL-3.0		5 tools Tool Name Description Trycycler subsample 0.5.5 Trycycler subsample: make a maximally-independent read subsets of an appropiate depth for your genome Trycycler partition 0.5.5 Trycycler partition: assign the reads to the clusters Trycycler cluster 0.5.5 Trycycler cluster: cluster the contigs of your input assemblies into per-replicon groups Trycycler consensus 0.5.5 Trycycler consensus: generate a consensus contig sequence for each cluster Trycycler reconcile/msa 0.5.5 Trycycler reconcile/msa: reconcile the contigs within each cluster and perform a multiple sequence alignment
UCSC tools	Utilities for handling sequences and assemblies from the UCSC Genome Browser project.		ucsc	Sequence analysis			Other		6 tools Tool Name Description faSplit 377 faSplit: Split a FASTA file wigtobigwig 447+galaxy0 wigtobigwig: bedGraph or Wig to bigWig converter faToVcf 448+galaxy0 faToVcf: Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs twoBitToFa 377 twoBitToFa: Convert all or part of .2bit file to FASTA Convert GTF to BED12 357 Convert GTF to BED12: BED-to-bigBed 1.0.1 BED-to-bigBed: converter
umi_tools	Tools for handling Unique Molecular Identifiers in NGS data sets.		umi_tools	NGS Sequence sites, features and motifs Quality affairs	UMI-tools: Modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy		MIT		5 tools Tool Name Description UMI-tools whitelist 1.1.2+galaxy2 UMI-tools whitelist: Extract cell barcodes from FASTQ files UMI-tools group 1.1.2+galaxy2 UMI-tools group: Extract UMI from fastq files UMI-tools count 1.1.2+galaxy2 UMI-tools count: performs quantification of UMIs from BAM files UMI-tools extract 1.1.2+galaxy2 UMI-tools extract: Extract UMI from fastq files UMI-tools deduplicate 1.1.2+galaxy2 UMI-tools deduplicate: Extract UMI from fastq files
Unicycler	A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads.		unicycler	Microbiology Genomics Sequencing Sequence assembly	Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads	Unicycler	GPL-3.0		Create assemblies with Unicycler 0.5.1+galaxy0
unipept	Metaproteomics data analysis with a focus on interactive data visualizations.		unipept	Proteomics Proteogenomics Biodiversity Workflows	2 publications Publications Unipept web services for metaproteomics analysis Unipept Desktop: A Faster, More Powerful Metaproteomics Results Analysis Tool		MIT		Unipept 4.5.1
UniProt_Downloader	The universal protein knowledgebase in 2021. You are using a version of browser that may not display all the features of this website.		UniProt_Downloader	Proteomics Sequence analysis Literature and language Model organisms Proteomics experiment	14 publications Publications UniProt: the universal protein knowledgebase in 2021 Reorganizing the protein space at the Universal Protein Resource (UniProt) The Universal Protein resource (UniProt) 2009 The universal protein resource (UniProt) in 2010 The Universal Protein Resource (UniProt) The Universal Protein Resource (UniProt) The Universal Protein Resource (UniProt): an expanding universe of protein information. The Universal Protein resource (UniProt) UniProt Knowledgebase: A hub of integrated protein data UniProt: A worldwide hub of protein knowledge 10.1093/nar/gkh131 UniProt: The universal protein knowledgebase Erratum: UniProt: The universal protein knowledgebase (Nucleic Acids Research (2017) 45 (D158-D169) DOI: 10.1093/nar/gkw1099) Update on activities at the Universal Protein Resource (UniProt) in 2013		CC-BY-4.0		UniProt 2.4.0
uniprot_rest_interface	The universal protein knowledgebase in 2021. You are using a version of browser that may not display all the features of this website.		uniprot_rest_interface	Proteomics Sequence analysis Literature and language Model organisms Proteomics experiment	14 publications Publications UniProt: the universal protein knowledgebase in 2021 Reorganizing the protein space at the Universal Protein Resource (UniProt) The Universal Protein resource (UniProt) 2009 The universal protein resource (UniProt) in 2010 The Universal Protein Resource (UniProt) The Universal Protein Resource (UniProt) The Universal Protein Resource (UniProt): an expanding universe of protein information. The Universal Protein resource (UniProt) UniProt Knowledgebase: A hub of integrated protein data UniProt: A worldwide hub of protein knowledge 10.1093/nar/gkh131 UniProt: The universal protein knowledgebase Erratum: UniProt: The universal protein knowledgebase (Nucleic Acids Research (2017) 45 (D158-D169) DOI: 10.1093/nar/gkw1099) Update on activities at the Universal Protein Resource (UniProt) in 2013		CC-BY-4.0		UniProt 0.6
unzip			unzip						Unzip 6.0+galaxy0				6.0-gcccore-10.3.06.0-gcccore-11.3.06.0-gcccore-12.3.0 (D) 6.0-gcccore-10.3.06.0-gcccore-11.3.06.0-gcccore-12.3.0 (D) 6.0-gcccore-10.3.06.0-gcccore-11.3.06.0-gcccore-12.3.0 (D)
Variant Effect Predictor (VEP)	Tool for predicting effects of variants for any genome in Ensembl or with genome annotation (via GFF). This includes vertebrates and also plants, fungi, protists, metazoa and bacteria. There is a web and a REST API version but the most powerful is the Perl script version. See McLaren et al., 2016, Genome Biology		vep	Genetic variation Genomics	The Ensembl Variant Effect Predictor		Apache-2.0						107-gcc-11.3.0
VarScan	VarScan, an open source tool for variant detection that is compatible with several short read align-ers.		varscan	Sequencing DNA polymorphism	2 publications Publications VarScan: Variant detection in massively parallel sequencing of individual and pooled samples VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing	VarScan			4 tools Tool Name Description VarScan copynumber 2.4.3.2 VarScan copynumber: Determine relative tumor copy number from tumor-normal pileups VarScan mpileup 2.4.3.1 VarScan mpileup: for variant detection VarScan somatic 2.4.3.6 VarScan somatic: Call germline/somatic and LOH variants from tumor-normal sample pairs VarScan 2.4.2 VarScan: for variant detection
vcflib	API and command line utilities for the manipulation of VCF files.		vcflib	Genomics Data management	10.1101/023754		MIT		23 tools Tool Name Description VCFtoTab-delimited: 1.0.0_rc3+galaxy0 VCFtoTab-delimited:: Convert VCF data into TAB-delimited format VCFaddinfo: 1.0.0_rc3+galaxy0 VCFaddinfo:: Adds info fields from the second dataset which are not present in the first dataset VcfAllelicPrimitives: 1.0.0_rc3+galaxy0 VcfAllelicPrimitives:: Split alleleic primitives (gaps or mismatches) into multiple VCF lines VCFannotate: 1.0.0_rc3+galaxy0 VCFannotate:: Intersect VCF records with BED annotations VCFannotateGenotypes: 1.0.0_rc3+galaxy0 VCFannotateGenotypes:: Annotate genotypes in a VCF dataset using genotypes from another VCF dataset VCF-BEDintersect: 1.0.0_rc3+galaxy0 VCF-BEDintersect:: Intersect VCF and BED datasets VCFbreakCreateMulti: 1.0.0_rc3+galaxy0 VCFbreakCreateMulti:: Break multiple alleles into multiple records, or combine overallpoing alleles into a single record VCFcheck: 1.0.0_rc3+galaxy0 VCFcheck:: Verify that the reference allele matches the reference genome VCFcombine: 1.0.0_rc3+galaxy0 VCFcombine:: Combine multiple VCF datasets VCFcommonSamples: 1.0.0_rc3+galaxy0 VCFcommonSamples:: Output records belonging to samples common between two datasets VCFdistance: 1.0.0_rc3+galaxy0 VCFdistance:: Calculate distance to the nearest variant VCFfilter: 1.0.0_rc3+galaxy3 VCFfilter:: filter VCF data in a variety of attributes VCFfixup: 1.0.0_rc3+galaxy0 VCFfixup:: Count the allele frequencies across alleles present in each record in the VCF file VCFflatten: 1.0.0_rc3+galaxy0 VCFflatten:: Removes multi-allelic sites by picking the most common alternate VCFgenotype-to-haplotype: 1.0.0_rc3+galaxy0 VCFgenotype-to-haplotype:: Convert genotype-based phased alleles into haplotype alleles VCFgenotypes: 1.0.0_rc3+galaxy0 VCFgenotypes:: Convert numerical representation of genotypes to allelic VCFhetHomAlleles: 1.0.0_rc3+galaxy0 VCFhetHomAlleles:: Count the number of heterozygotes and alleles, compute het/hom ratio VCFleftAlign: 1.0.0_rc3+galaxy0 VCFleftAlign:: Left-align indels and complex variants in VCF dataset VCFprimers: 1.0.0_rc3+galaxy0 VCFprimers:: Extract flanking sequences for each VCF record VCFrandomSample: 1.0.0_rc3+galaxy0 VCFrandomSample:: Randomly sample sites from VCF dataset VCFselectsamples: 1.0.0_rc3+galaxy0 VCFselectsamples:: Select samples from a VCF dataset VCFsort: 1.0.0_rc3+galaxy0 VCFsort:: Sort VCF dataset by coordinate VCF-VCFintersect: 1.0.0_rc3+galaxy0 VCF-VCFintersect:: Intersect two VCF datasets				1.0.3-foss-2021a-r-4.1.0
VCFTools	Provide easily accessible methods for working with complex genetic variation data in the form of VCF files.		vcftools	Genetic variation	The variant call format and VCFtools	VCFTools	GPL-3.0		2 tools Tool Name Description Intersect 0.1.1 Intersect: multiple VCF datasets Merge 0.1.1 Merge: multiple VCF datasets		0.1.16	0.1.16--pl5321h9a82719_6	0.1.16-gcc-10.3.00.1.16-gcc-11.3.0 (D) 0.1.16-gcc-10.3.00.1.16-gcc-11.3.0 (D)
Velvet	A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD.		velvet	Sequence assembly	10.1101/gr.074492.107	Velvet	GPL-3.0		3 tools Tool Name Description velvetg 1.2.10.2 velvetg: Velvet sequence assembler for very short reads velveth 1.2.10.3 velveth: Prepare a dataset for the Velvet velvetg Assembler VelvetOptimiser 2.2.6+galaxy2 VelvetOptimiser: Automatically optimize Velvet assemblies	1.2.10		1.2.10--h7132678_5
verkko			verkko								1.1
VisIt			visit							3.1.2
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.		vsearch	Metagenomics Sequence analysis	10.7717/peerj.2584	vsearch	GPL-3.0		8 tools Tool Name Description VSearch clustering 2.8.3.0 VSearch clustering: VSearch masking 2.8.3.0 VSearch masking: VSearch dereplication 2.8.3.0 VSearch dereplication: VSearch chimera detection 2.8.3.0 VSearch chimera detection: VSearch search 2.8.3.1 VSearch search: VSearch sorting 2.8.3.0 VSearch sorting: VSearch alignment 2.8.3.0 VSearch alignment: VSearch shuffling 2.8.3.0 VSearch shuffling:
weblogo3			weblogo3						Sequence Logo 3.5.0
WhatsHap	Software for phasing genomic variants using DNA sequencing reads, also called haplotype assembly. It is especially suitable for long reads, but works also well with short reads.		whatshap	DNA polymorphism Sequence assembly	2 publications Publications WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads 10.1101/037101		MIT				1.72.3 1.72.3
WindowMasker	windowmasker identifies and masks highly repetitive DNA sequences in a genome, using only the sequence of the genome itself.		windowmasker	Sequencing					2 tools Tool Name Description WindowMasker ustat 1.0 WindowMasker ustat: Mask sequences using a WindowMasker unit counts table WindowMasker mkcounts 1.0 WindowMasker mkcounts: Construct WindowMasker unit counts table
winnowmap	Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. Winnowmap development began on top of minimap2 codebase, and since then we have incorporated the following two ideas to improve mapping accuracy within repeats		winnowmap	Mapping	2 publications Publications Long-read mapping to repetitive reference sequences using Winnowmap2 Weighted minimizer sampling improves long read mapping		Not licensed				2.03
Workflow 4 Metabolomics	First fully open-source and collaborative online platform for computational metabolomics. It includes preprocessing, normalization, quality control, statistical analysis of LC/MS, FIA-MS, GC/MS and NMR data.		workflow4metabolomics	Systems biology Metabolomics Computational biology	2 publications Publications Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics Create, run, share, publish, and reference your LC–MS, FIA–MS, GC–MS, and NMR data analysis workflows with the Workflow4Metabolomics 3.0 Galaxy online infrastructure for metabolomics				19 tools Tool Name Description Determine_batch_correction 2.1.2 Determine_batch_correction: to choose between linear, lowess and loess methods Batch_correction 2.1.2 Batch_correction: Corrects intensities for signal drift and batch-effects Check Format 3.0.0 Check Format: Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files Generic_Filter 2017.06 Generic_Filter: Removes elements according to numerical or qualitative values HMDB MS search 1.6.1 HMDB MS search: search by masses on HMDB online LCMS bank LCMS matching 4.0.2 LCMS matching: Annotation of LCMS peaks using matching on a in-house spectra database or on PeakForest spectra database. MSnbase readMSData 2.8.2.1 MSnbase readMSData: Imports mass-spectrometry data files NMR spectra alignment 2.0.4 NMR spectra alignment: based on the Cluster-based Peak Alignment (CluPA) algorithm NMR_Bucketing 2.0.3 NMR_Bucketing: Bucketing and integration of NMR Bruker raw data NMR_Read 3.3.0 NMR_Read: Read Bruker NMR raw files NMR_Preprocessing 3.3.0 NMR_Preprocessing: Preprocessing of 1D NMR spectra Normalization 2.0.1 Normalization: Normalization of (preprocessed) spectra Quality Metrics 2.2.8 Quality Metrics: Metrics and graphics to check the quality of the data Table Merge 1.0.1 Table Merge: Merging dataMatrix with a metadata table Univariate 2.2.4 Univariate: Univariate statistics W4m Data Subset 0.98.11 W4m Data Subset: Filter W4m data by values or metadata OPLS-DA_Contrasts 0.98.17 OPLS-DA_Contrasts: OPLS-DA Contrasts of Univariate Results Join +/- Ions 0.98.2 Join +/- Ions: Join positive and negative ionization-mode W4M datasets for the same samples Multilevel 0.5.0 Multilevel: Data transformation: Within matrix decomposition for repeated measurements (cross-over design) with mixOmics package
wormbase	Caenorhabditis elegans genome database. International consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes. Founded in 2000, the Consortium is led by Paul Sternberg of CalTech, Paul Kersey of the EBI, Matt Berriman of the Wellcome Trust Sanger Institute, and Lincoln Stein of the Ontario Institute for Cancer Research.		wormbase	Model organisms	WormBase 2014: New views of curated biology				WormBase 1.0.1
xarray			xarray						2 tools Tool Name Description NetCDF xarray Metadata Info 0.15.1 NetCDF xarray Metadata Info: summarize content of a Netcdf file NetCDF xarray Selection 0.15.1 NetCDF xarray Selection: extracts variable values with custom conditions on dimensions
xcms	Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. The packages enables imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files and preprocesses data for high-throughput, untargeted analyte profiling.		xcms	Biological imaging Data visualisation Metabolomics	Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data		GPL-2.0		10 tools Tool Name Description xcms plot raw 4.0.0+galaxy0 xcms plot raw: Plot raw data filtered by m/z range and retention time (RT) range xcms plot eic 4.0.0+galaxy0 xcms plot eic: Plot the extracted ion chromatogram (EIC) from mzML file xcms get a sampleMetadata file 3.4.4.0 xcms get a sampleMetadata file: which need to be filled with extra information xcms fillChromPeaks (fillPeaks) 3.4.4.0 xcms fillChromPeaks (fillPeaks): Integrate areas of missing peaks xcms groupChromPeaks (group) 3.4.4.0 xcms groupChromPeaks (group): Perform the correspondence, the grouping of chromatographic peaks within and between samples. xcms findChromPeaks Merger 3.4.4.0 xcms findChromPeaks Merger: Merge xcms findChromPeaks RData into a unique file to be used by group xcms plot chromatogram 3.4.4.0 xcms plot chromatogram: Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s) xcms adjustRtime (retcor) 3.4.4.1 xcms adjustRtime (retcor): Retention Time Correction xcms process history 3.4.4.0 xcms process history: Create a summary of XCMS analysis xcms findChromPeaks (xcmsSet) 3.4.4.1 xcms findChromPeaks (xcmsSet): Chromatographic peak detection
xml4ena			xml4ena
xpore	Detection of differential RNA modifications from direct RNA sequencing of human cell lines. Python package for detection of differential RNA modifications from direct RNA sequencing.		xpore	RNA-Seq RNA Gene expression Genotype and phenotype Molecular interactions, pathways and networks	10.1101/2020.06.18.160010	xpore	MIT						2.1--pyh5e36f6f_0
xtandem	Matches tandem mass spectra with peptide sequences.		xtandem	Proteomics Proteomics experiment	TANDEM: Matching proteins with tandem mass spectra	xtandem			2 tools Tool Name Description X!Tandem MSMS Search 1.1.1 X!Tandem MSMS Search: Run an X!Tandem Search Tandem to pepXML 1.1.1 Tandem to pepXML: Converts a tandem result file to pepXML
YaHS	YaHS is scaffolding tool using Hi-C data. It relies on a new algorithm for contig joining detection which considers the topological distribution of Hi-C signals aiming to distinguish real interaction signals from mapping noises.		yahs	Sequence assembly DNA binding sites	10.1101/2022.06.09.495093		MIT		YAHS 1.2a.2+galaxy2		1.1
yeastmine	Search and retrieve S. cerevisiae data, populated by SGD and powered by InterMine		yeastmine	Data management Genomics Proteomics	InterMine: A flexible data warehouse system for the integration and analysis of heterogeneous biological data		LGPL-2.1		YeastMine 1.0.0
zebrafishmine	ZebrafishMine is powered by the InterMIne data warehouse system, and integrates biological data sets from multiple sources. It currently includes updates of data from ZFIN, the zebrafish model organism database. There is also data from the Panther database.		zebrafishmine	Data management Genomics Proteomics	InterMine: A flexible data warehouse system for the integration and analysis of heterogeneous biological data		LGPL-2.1		ZebrafishMine 1.0.0