Available Software for Swan

Tip

HCC provides some software packages via the Apptainer container software. If you do not see a desired package in the module list below, please check the Using Apptainer page for the software list there.

Module prerequisites

If a module lists one or more prerequisites, the prerequisite module(s) must be loaded before or along with, that module.

For example, the cdo/2.1 modules requires compiler/pgi/13. To load the cdo module, doing either

module load compiler/pgi/13

module load cdo/2.1

or

module load compiler/pgi/13 cdo/2.1 (Note the prerequisite module must be first.)

is acceptable.

Multiple versions

Some packages list multiple compilers for prerequisites. This means that the package has been built with each version of the compilers listed.

Custom GPU Anaconda Environment

If you are using custom GPU Anaconda Environment, the only module you need to load is anaconda:

module load anaconda

last generated 2025-05-31T05:03:18CDT

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Name	Version	Module Name	Prerequisites	Type	Domain	Description
3d-dna	201008	3d-dna/201008	None	application	computational biology	3D de novo assembly (3D-DNA) pipeline.
3dslicer	4.11.20210226	3dslicer/4.11.20210226	None	application	biomedicine	3D Slicer is a free, open source and multi-platform software package widely used for medical, biomedical, and related imaging research.
BICseq	1.1.2	BICseq/1.1	None	application	computational biology	BIC-seq can accurately and efficiently identify CNVs via minimizing the Bayesian information criterion.
CNVnator	0.4.1	CNVnator/0.4	None	application	genotyping	CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
GSL	2.6	GSL/2.6	compiler/gcc/10 compiler/pgi/20 compiler/intel/20 compiler/intel/19 compiler/gcc/11	library	runtime support
LIS	7.3	LIS/7.3	compiler/intel/19:openmpi/4.0	application	Simulation
MEME	4.11.2	MEME/4.11	compiler/gcc/11:openmpi/4.1	application	computational biology	The MEME suite is a collection of tools for the discovery and analysis of sequence motifs. It is hosted at http://meme-suite.org/.
MEME	5.5.5	MEME/5.5	compiler/gcc/11:openmpi/4.1	application	computational biology	The MEME suite is a collection of tools for the discovery and analysis of sequence motifs. It is hosted at http://meme-suite.org/.
NCL	6.1	NCL/6.1	None	application	utility	NCAR Command Language
NCL	6.3	NCL/6.3	None	application	utility	NCAR Command Language
NCL	6.4	NCL/6.4	None	application	utility	NCAR Command Language
NCL	6.6.2	NCL/6.6	None	application	utility	NCAR Command Language
NCO	4.9.4	NCO/4.9	compiler/pgi/20	library	runtime support
NCO	4.9.9	NCO/4.9	compiler/intel/20	library	runtime support
NUWRF	v9	NUWRF/intel/v9	None	library	runtime support
R	3.4.4	R/3.4	None	library	runtime support	R is a free software environment for statistical computing and graphics.
R	3.5.1	R/3.5	None	library	runtime support	R is a free software environment for statistical computing and graphics.
R	3.6.3	R/3.6	None	library	runtime support	R is a free software environment for statistical computing and graphics.
R	4.0.5	R/4.0	None	library	runtime support	R is a free software environment for statistical computing and graphics.
R	4.1.3	R/4.1	None	library	runtime support	R is a free software environment for statistical computing and graphics.
R	4.2.2	R/4.2	None	library	runtime support	R is a free software environment for statistical computing and graphics.
R	4.3.3	R/4.3	None	library	runtime support	R is a free software environment for statistical computing and graphics.
RAPSearch2	2.19	RAPSearch2/2.19	None	application	computational biology	RAPSearch2 is a tool for fast protein similarity searches.
SRAtoolkit	2.10.0	SRAtoolkit/2.10	None	application	computational biology	SRA Toolkit and SDK from NCBI
SRAtoolkit	2.11.0	SRAtoolkit/2.11	None	application	computational biology	SRA Toolkit and SDK from NCBI
SRAtoolkit	2.8.2	SRAtoolkit/2.8	None	application	computational biology	SRA Toolkit and SDK from NCBI
SRAtoolkit	2.9.6	SRAtoolkit/2.9	None	application	computational biology	SRA Toolkit and SDK from NCBI
StringTie	1.3.0	StringTie/1.3	None	application	computational biology	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
StringTie	2.1.2	StringTie/2.1	None	application	computational biology	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
StringTie	2.2.1	StringTie/2.2	None	application	computational biology	StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
TrimGalore	0.4.5	TrimGalore/0.4	None	library	runtime support
WRF	v3	WRF/v3	compiler/pgi/20:openmpi/4.0	library	runtime support
WRF	v4	WRF/v4	compiler/pgi/20:openmpi/4.0 compiler/intel/20:openmpi/4.0	library	runtime support
abacas	1.3.1	abacas/1.3	None	application	computational biology	ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence.
abaqus	2021	abaqus/2021	None	application	Engineering	Abaqus is a software suite for finite element analysis and computer-aided engineering.
abayesqr	1.0	abayesqr/1.0	None	application	high-throughput sequencing data	aBayesQR is a viral quasispecies reconstruction algorithm that employs a maximum-likelihood framework to infer individual sequences in a mixture from high-throughput sequencing data.
abinit	9.6.2	abinit/9.6	compiler/gcc/10:openmpi/4.1	application	Physics	ABINIT is an atomic-scale simulation software suite.
abricate	0.8.13	abricate/0.8	None	application	Biology	Mass screening of contigs for antibiotic resistance genes
abricate	1.0.1	abricate/1.0	None	application	Biology	Mass screening of contigs for antibiotic resistance genes
adfr-suite	1.0	adfr-suite/1.0	None	application	Chemistry	AutoDockFR (or ADFR in short) is a protein-ligand docking program developed in the Sanner laboratory at Scripps Research under the AutoDock umbrella
admixtools	7.0.2	admixtools/7.0	None	application	admixture	ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.
admixture	1.3.0	admixture/1.3	None	application	admixture	ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.
afni	18.2.06	afni/18.2	None	application	MRI	AFNI is a suite of programs for looking at and analyzing 3D brain images.
afni	21.1.06	afni/21.1	None	application	MRI	AFNI is a suite of programs for looking at and analyzing 3D brain images.
afni	22.0.21	afni/22.0	None	application	MRI	AFNI is a suite of programs for looking at and analyzing 3D brain images.
afni	23.1.10	afni/23.1	None	application	MRI	AFNI is a suite of programs for looking at and analyzing 3D brain images.
afq	a42e157	afq/a42e157	None	application	matlab toolbox	Automated Fiber Quantification.
afq	c59f21b	afq/c59f21b	None	application	matlab toolbox	Automated Fiber Quantification.
afterqc	0.9.6	afterqc/0.9	None	application	package	Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data. AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair. Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq...and other Illumina 1.8 or newer formats.
agat	0.9.2	agat/0.9	None	application	bioinformatics	Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.
agfusion	1.0	agfusion/1.0	None	application	Biology	AGFusion is a python package for annotating gene fusions from the human or mouse genomes.
agfusion	1.251	agfusion/1.251	None	application	Biology	AGFusion is a python package for annotating gene fusions from the human or mouse genomes.
agouti	1.0.3	agouti/py39/1.0	None	application	computational biology	Annotation of Genomic and Transcriptomic Intervals
aligngraph	1.0	aligngraph/1.0	None	application	computational biology
allinea	18.0	allinea/18.0	None	application	Utility
allinea	18.2	allinea/18.2	None	application	Utility
allinea	19.0	allinea/19.0	None	application	Utility
allinea	21.0	allinea/21.0	None	application	Utility
allinea	22.0	allinea/22.0	None	application	Utility
allinea	22.1	allinea/22.1	None	application	Utility
allinea	4.2	allinea/4.2	None	application	Utility
allinea	5.0	allinea/5.0	None	application	Utility
allinea	5.1	allinea/5.1	None	application	Utility
allinea	6.0	allinea/6.0	None	application	Utility
allinea	6.1	allinea/6.1	None	application	Utility
allinea	7.0	allinea/7.0	None	application	Utility
alphafold3	3.0.1	alphafold3/3.0	None	application	computational biology	AlphaFold 3 inference pipeline.
ambertools	22	ambertools/22	compiler/gcc/10:openmpi/4.1	application	computational chemistry
ambertools	23	ambertools/23	compiler/gcc/11:openmpi/4.1 compiler/gcc/10:openmpi/4.1	application	computational chemistry
ambertools	24	ambertools/24	compiler/gcc/10:openmpi/4.1 compiler/gcc/11:openmpi/4.1	application	computational chemistry
amorph	2021.05.10	amorph/2021.05.10	None	application	environment	AMORPH utilizes a new Bayesian statistical approach to interpreting X-ray diffraction results of samples with both crystalline and amorphous components.
amos	3.1.0	amos/3.1	None	application	computational biology	A Modular, Open-Source whole genome assembler
anaconda	2.7	anaconda/2.7	None	application	system
anaconda	23.1.0/1.3.1	anaconda/23.1	None	application	system
anaconda	23.11.0/1.5.4	anaconda/23.11	None	application	system
anaconda	23.7.2/1.4.9	anaconda/23.7	None	application	system
anaconda	3.3	anaconda/3.3	None	application	system
anaconda	3.4	anaconda/3.4	None	application	system
anaconda	4.10.3	anaconda/4.10	None	application	system
anaconda	4.12.0/0.24.0	anaconda/4.12	None	application	system
anaconda	4.3	anaconda/4.3	None	application	system
anaconda	4.6	anaconda/4.6	None	application	system
anaconda	4.8	anaconda/4.8	None	application	system
anaconda	4.9.2	anaconda/4.9	None	application	system
angsd	0.935	angsd/0.935	None	application	Bioinformatics	ANGSD: Analysis of next generation Sequencing Data
angsd	0.937	angsd/0.937	None	application	Bioinformatics	ANGSD: Analysis of next generation Sequencing Data
ansys	19.2	ansys/19.2	None	application	Engineering	ANSYS offers a comprehensive software suite that spans the entire range of physics, providing access to virtually any field of engineering simulation that a design process requires.
ansys	2021R2	ansys/2021	None	application	Engineering	ANSYS offers a comprehensive software suite that spans the entire range of physics, providing access to virtually any field of engineering simulation that a design process requires.
ant	1.10.1	ant/1.10	None	library	java	Java build tool
ant	1.9.9	ant/1.9	None	library	java	Java build tool
antismash	6.1.0	antismash/6.1	None	application	Biology	antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell
ants	2.5.1	ants/2.5	None	application	computational neuroimaging	ANTs computes high-dimensional mappings to capture the statistics of brain structure and function.
anvio	6.1	anvio/6.1	None	application	Omics	A platform for integrated multi-omics
anvio	6.2	anvio/6.2	None	application	Omics	A platform for integrated multi-omics
anvio	7	anvio/7	None	application	Omics	A platform for integrated multi-omics
anvio	7.1	anvio/7.1	None	application	Omics	A platform for integrated multi-omics
apkid	1.0.0	apkid/1.0	None	application	Malware	APKiD is Android Application Identifier for Packers, Protectors, Obfuscators and Oddities - PEiD for Android.
apptainer	1.1	apptainer/1.1	None	application	system	Application containers enabling mobility of compute.
aria2	1.23.0	aria2/1.23	None	application	tool	aria2 is a lightweight multi-protocol & multi-source command-line download utility.
aria2	1.34.0	aria2/1.34	None	application	tool	aria2 is a lightweight multi-protocol & multi-source command-line download utility.
aria2	1.36.0	aria2/1.36	None	application	tool	aria2 is a lightweight multi-protocol & multi-source command-line download utility.
aria2	1.37.0	aria2/1.37	None	application	tool	aria2 is a lightweight multi-protocol & multi-source command-line download utility.
arpack-ng	3.9.1	arpack-ng/3.9	compiler/intel/20:openmpi/4.1	library	runtime support
arriba	2.4.0	arriba/2.4	None	application	computational biology	Fast and accurate gene fusion detection from RNA-Seq data
art	2.6.0	art/2.6	None	application	computational biology	ART is a set of simulation tools to generate synthetic next-generation sequencing reads.
art	2016.06.05	art/2016.06.05	None	application	computational biology	ART is a set of simulation tools to generate synthetic next-generation sequencing reads.
ase	3.18.1	ase/3.18	None	application	Physics	ASE is a python package providing an open source Atomic Simulation Environment in the Python language.
ashs	1.0.0	ashs/1.0	None	application	MRI	ASHS is software for automatic segmentation of the medial temporal lobe (MTL) substructures from brain MRI scans.
ashs	2.0.0	ashs/2.0	None	application	MRI	ASHS is software for automatic segmentation of the medial temporal lobe (MTL) substructures from brain MRI scans.
aspera-cli	3.7.7	aspera-cli/3.7	None	application	system	IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line.
aspera-cli	4.14.0	aspera-cli/4.14	None	application	system	IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line.
asreml	3.0	asreml/3.0	None	application	data analysis	ASReml
asreml	4.1	asreml/4.1	None	application	data analysis	ASReml
asreml	4.2	asreml/4.2	None	application	data analysis	ASReml
assembly-stats	1.0.1	assembly-stats/1.0	None	application	bioinformatics	Get assembly statistics from FASTA and FASTQ files
atat	3.36	atat/3.36	compiler/gcc/11	application	Chemistry
atk	2016.3	atk/2016.3	None	application	Chemistry
atomate2	0.0.10	atomate2/py38/0.0.10	None	application	Simulation	atomate2 is a library of materials science workflows
atomate2	0.0.10	atomate2/py39/0.0.10	None	application	Simulation	atomate2 is a library of materials science workflows
atomate2	0.0.10	atomate2/py310/0.0.10	None	application	Simulation	atomate2 is a library of materials science workflows
atsas	3.2.1	atsas/3.2	None	application	molecular simulation	A program suite for small-angle scattering data analysis from biological macromolecules.
augur	12.0.0	augur/12.0	None	application	public health	Process pathogen genome data for the Nextstrain platform
augustus	3.0	augustus/3.0	None	application	computational biology	AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
augustus	3.2.3	augustus/3.2	None	application	computational biology	AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
augustus	3.3	augustus/3.3	None	application	computational biology	AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
augustus	3.4	augustus/3.4	None	application	computational biology	AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
augustus	3.5.0	augustus/3.5	None	application	computational biology	AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
autoconf	1.0	autoconf/2.69	None	application	Utilities	The autotools collection is a set of tools that make it easy to build and install programs from a source distribution.
autodock	4.2.6	autodock/4.2	None	application	Chemistry	AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
autodock-gpu	1.2	autodock-gpu/1.2	None	application	Chemistry	AutoDock for GPUs using CUDA.
autodock-gpu	1.3	autodock-gpu/1.3	None	application	Chemistry	AutoDock for GPUs using CUDA.
autodock-gpu	1.4.3	autodock-gpu/1.4	None	application	Chemistry	AutoDock for GPUs using CUDA.
autodock-gpu	1.5.3	autodock-gpu/1.5	None	application	Chemistry	AutoDock for GPUs using CUDA.
autodock-gpu	2024.03.05	autodock-gpu/2024.03.05	None	application	Chemistry	AutoDock for GPUs using CUDA.
autodock-gpu	4.2.6.c135512	autodock-gpu/4.2	None	application	Chemistry	AutoDock for GPUs using CUDA.
autodock-vina	1.1.2	autodock-vina/1.1	None	application	Chemistry	AutoDock Vina is an open-source program for doing molecular docking
automake	1.0	automake/1.16	None	application	Utilities	The autotools collection is a set of tools that make it easy to build and install programs from a source distribution.
autotools	1.0	autotools/1.0	None	application	Utilities	The autotools collection is a set of tools that make it easy to build and install programs from a source distribution.
awscli	1.1.120	awscli/1.11	None	application	utility	Universal Command Line Environment for AWS.
awscli	1.19.5	awscli/1.19	None	application	utility	Universal Command Line Environment for AWS.
awscli	1.23.6	awscli/1.23	None	application	utility	Universal Command Line Environment for AWS.
azcopy	7.2.0	azcopy/7.2	None	application	Utility	AzCopy is a command-line utility designed for copying data to/from Microsoft Azure Blob and File storage, using simple commands designed for optimal performance.
bakta	1.9.4	bakta/1.9	None	application	computational biology	Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.
ballgown	2.2.0	ballgown/2.2	None	application	computational biology	Ballgown is a software package designed to facilitate flexible differential expression analysis of RNA-Seq data. It also provides functions to organize, visualize, and analyze the expression measurements for your transcriptome assembly.
bam-readcount	0.6	bam-readcount/0.6	None	application	computational biology	The purpose of this program is to generate metrics at single nucleotide positions.
bam-readcount	0.8	bam-readcount/0.8	None	application	computational biology	The purpose of this program is to generate metrics at single nucleotide positions.
bamm	1.7.3	bamm/1.7	None	application	computational biology	Metagenomics-focused BAM file manipulation
bamscale	0.0.5	bamscale/0.0.5	None	application	computational biology	BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks
bamtools	2.3.0	bamtools/2.3	None	application	computational biology	C++ API & command-line toolkit for working with BAM data
bamtools	2.4.1	bamtools/2.4	None	application	computational biology	C++ API & command-line toolkit for working with BAM data
bamtools	2.5.1	bamtools/2.5	None	application	computational biology	C++ API & command-line toolkit for working with BAM data
basespace-cli	1.1.0	basespace-cli/1.1	None	application	biology	Toolkit to perform regulatory genomics data analysis
basetools/gapfiller	1.10	basetools/gapfiller/1.10	None	application	computational biology	GapFiller is a stand-alone program for closing gaps within pre-assembled scaffolds.
basetools/sspace-standard	3.0	basetools/sspace-standard/3.0	None	application	computational biology	SSPACE-standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data.
bayespeak	1.24.0	bayespeak/1.24.0	None	application	computational biology	This package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.
bbmap	37.17	bbmap/37.17	None	application	computational biology	BBMap is a splice-aware global aligner for DNA and RNA sequencing reads.
bbmap	38.06	bbmap/38.06	None	application	computational biology	BBMap is a splice-aware global aligner for DNA and RNA sequencing reads.
bbmap	38.84	bbmap/38.84	None	application	computational biology	BBMap is a splice-aware global aligner for DNA and RNA sequencing reads.
bbmap	39.06	bbmap/39.06	None	application	computational biology	BBMap is a splice-aware global aligner for DNA and RNA sequencing reads.
bc	1.07.1	bc/1.07	None	application	Utility	bc is an arbitrary precision numeric processing language.
bcftools	1.10.2	bcftools/1.10	None	application	computational biology	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.
bcftools	1.17	bcftools/1.17	None	application	computational biology	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.
bcftools	1.2	bcftools/1.2	None	application	computational biology	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.
bcftools	1.21	bcftools/1.21	None	application	computational biology	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.
bcftools	1.3.1	bcftools/1.3	None	application	computational biology	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.
bcftools	1.8	bcftools/1.8	None	application	computational biology	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.
bcftools	1.9	bcftools/1.9	None	application	computational biology	BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.
bcl2fastq	1.8.4	bcl2fastq/1.8	None	application	biology	bcl2fastq can be used to demultiplex data and convert BCL files to FASTQ file formats for downstream analysis
bcl2fastq2	2.20.0.422	bcl2fastq2/2.20	None	application	computational biology	The Illumina bcl2fastq2 Conversion Software v2.20 demultiplexes sequencing data and converts base call (BCL) files into FASTQ files.
beagle	4.1_21Jan17.6cc	beagle/4.1	None	application	Biology	Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
beagle	5.1_24Aug19.3e8	beagle/5.1	None	application	Biology	Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
beagle	5.2_21Apr21.304	beagle/5.2	None	application	Biology	Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
beagle-lib	4.0.0	beagle-lib/4.0	None	application	computational biology	general purpose library for evaluating the likelihood of sequence evolution on trees
beast	1.10	beast/1.10	None	application	biology	BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
beast	1.8	beast/1.8	None	application	biology	BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
beast2	2.4	beast2/2.4	None	application	biology	BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
beast2	2.6.3	beast2/2.6	None	application	biology	BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
beast2	2.7.5	beast2/2.7	None	application	biology	BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
bedops	2.4.35	bedops/2.4	None	application	computational biology	BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.
bedtools	2.24.0	bedtools/2.24	None	application	computational biology	A powerful toolset for genome arithmetic
bedtools	2.27.1	bedtools/2.27	None	application	computational biology	A powerful toolset for genome arithmetic
bertopic	0.13.0	bertopic/0.13	None	application	Modeling	BERTopic performs topic Modeling with state-of-the-art transformer models.
beta	1.0.7	beta/1.0	None	application	computational biology	Binding and Expression Target Analysis (BETA) is a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes.
bfc	r181	bfc/r181	None	application	Biology	BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data.
bicseq2-norm	0.2.4	bicseq2-norm/0.2	None	application	bioinformatics	BICseq2-norm is for normalizing potential biases in the sequencing data.
bicseq2-seg	0.7.2	bicseq2-seg/0.7	None	application	bioinformatics	BICseq2-seg is for detecting CNVs based on the normalized data given by BICseq2-norm.
bidscoin	4.0.0	bidscoin/py38/4.0	None	application	neuroimaging	Converts and organises raw MRI data-sets according to the Brain Imaging Data Structure (BIDS).
binutils	2.30	binutils/2.30	None	application	Utilities	The GNU Binutils are a collection of binary tools.
binutils	2.35.1	binutils/2.35	None	application	Utilities	The GNU Binutils are a collection of binary tools.
binutils	2.38	binutils/2.38	None	application	Utilities	The GNU Binutils are a collection of binary tools.
bioawk	1.0	bioawk/1.0	None	application	Biology	BWK awk modified for biological data
biobambam	2.0.183	biobambam/2.0	None	application	computational biology	Tools for early stage alignment file processing
bioconductor	3.11	bioconductor/4.0	None	application	computational biology	Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor	3.13	bioconductor/r41/3.13	None	application	computational biology	Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor	3.14	bioconductor/r41/3.14	None	application	computational biology	Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor	3.16	bioconductor/r42/3.16	None	application	computational biology	Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor	3.17	bioconductor/r43/3.17	None	application	computational biology	Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor	3.18	bioconductor/r43/3.18	None	application	computational biology	Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor	3.4	bioconductor/r34/3.6	None	application	computational biology	Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor	3.6	bioconductor/3.4	None	application	computational biology	Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor	3.8	bioconductor/r35/3.8	None	application	computational biology	Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor	3.8	bioconductor/3.8	None	application	computational biology	Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor	4.0	bioconductor/r40/3.11	None	application	computational biology	Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor-ballgown	2.2.0	bioconductor-ballgown/2.2	None	application	computational biology	Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.
bioconductor-jmosaics	1.10	bioconductor-jmosaics/1.10	None	application	computational biology	Joint analysis of multiple ChIP-Seq data sets.
biodata	1.0	biodata/1.0	None	application	computational biology	Static data resources for bioinformatics/computational biology.
biom-format	2.1.10	biom-format/2.1	None	application	computational biology	The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project.
bioperl	1.6.924	bioperl/1.6	None	application	computational biology	BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.
bioperl	1.7.8	bioperl/1.7	None	application	computational biology	BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.
biopython	1.70	biopython/py27/1.70	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.70	biopython/py35/1.70	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.70	biopython/py36/1.70	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.71	biopython/py27/1.71	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.71	biopython/py35/1.71	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.71	biopython/py36/1.71	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.74	biopython/py27/1.74	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.74	biopython/py37/1.74	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.76	biopython/py27/1.76	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.76	biopython/py37/1.76	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.77	biopython/py37/1.77	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.77	biopython/py38/1.77	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.79	biopython/py36/1.79	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.79	biopython/py37/1.79	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.79	biopython/py38/1.79	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.79	biopython/py39/1.79	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.81	biopython/py39/1.81	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.81	biopython/py310/1.81	None	application	biological computation	Collection of freely available tools for computational molecular biology
biopython	1.81	biopython/py311/1.81	None	application	biological computation	Collection of freely available tools for computational molecular biology
biosamtools	1.38	biosamtools/1.38	None	application	computational biology
biser	1.4	biser/1.4	None	application	computational biology	Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies.
bismark	0.14.2	bismark/0.14	None	application	computational biology	Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.
bismark	0.19.1	bismark/0.19	None	application	computational biology	Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.
bismark	0.24.1	bismark/0.24	None	application	computational biology	Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.
bison	3.7.5	bison/3.7	None	application	Utility	General purpose parser generator converting annotated context-free grammar to a deterministic LR/GLR parser.
blast	2.10.0	blast/2.10	None	application	computational biology	NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast	2.12.0	blast/2.12	None	application	computational biology	NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast	2.13.0	blast/2.13	None	application	computational biology	NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast	2.14.0	blast/2.14	None	application	computational biology	NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast	2.15.0	blast/2.15	None	application	computational biology	NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast	2.2.29	blast/2.2.29	None	application	computational biology	NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast	2.2.30	blast/2.2	None	application	computational biology	NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast	2.4.0	blast/2.4	None	application	computational biology	NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast	2.6.0	blast/2.6	None	application	computational biology	NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast	2.7.1	blast/2.7	None	application	computational biology	NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast-legacy	2.2.26	blast-legacy/2.2.26	None	application	computational biology	NCBI BLAST sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blat	35	blat/35x1	None	application	computational biology	BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments.
blat	35	blat/35	None	application	computational biology	BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments.
blat	36	blat/36	None	application	computational biology	BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments.
blender	4.2.0	blender/4.2	None	application	3D	Blender is a free and open-source 3D computer graphics software tool set.
blobtoolkit	4.1.4	blobtoolkit/py39/4.1	None	application	bioinformatics	Interactive quality assessment of genome assemblies.
blobtoolkit	4.1.4	blobtoolkit/py310/4.1	None	application	bioinformatics	Interactive quality assessment of genome assemblies.
blobtools	1.1.1	blobtools/1.1	None	application	Bioinformatics	Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
boa-bacfinder	0.0.2016.02.11	boa-bacfinder/2016.02.11	None	application	computational biology	Find bacteriocins in bacterial genomes
boost	1.44	boost/1.44	None	application	System Environment/Base	Boost provides free peer-reviewed portable C++ source libraries.
boost	1.55.0	boost/1.55.0	None	application	System Environment/Base	Boost provides free peer-reviewed portable C++ source libraries.
boost	1.66	boost/1.66	compiler/gcc/9 compiler/gcc/10	application	System Environment/Base	Boost provides free peer-reviewed portable C++ source libraries.
boost	1.69	boost/1.69	compiler/gcc/9	application	System Environment/Base	Boost provides free peer-reviewed portable C++ source libraries.
boost	1.75	boost/1.75	compiler/intel/20 compiler/intel/19 compiler/gcc/9 compiler/intel/18 compiler/intel/2021 compiler/gcc/10 compiler/gcc/11	application	System Environment/Base	Boost provides free peer-reviewed portable C++ source libraries.
boris2	3.0	boris2/3.0	None	application	Physics	Boris Computational Spintronics.
bowtie	1.0	bowtie/1.0	None	application	computational biology	Fast and sensitive read alignment
bowtie	1.1.2	bowtie/1.1	None	application	computational biology	Fast and sensitive read alignment
bowtie	1.3.1	bowtie/1.3	None	application	computational biology	Fast and sensitive read alignment
bowtie	2.2.8	bowtie/2.2	None	application	computational biology	Fast and sensitive read alignment
bowtie	2.3.5	bowtie/2.3	None	application	computational biology	Fast and sensitive read alignment
bowtie	2.4.4	bowtie/2.4	None	application	computational biology	Fast and sensitive read alignment
bowtie	2.5.4	bowtie/2.5	None	application	computational biology	Fast and sensitive read alignment
boxnotes2html	0.1.4	boxnotes2html/0.1	None	application	Utility	Converting from Box Notes to HTML or other formats
bracken	2.6.0	bracken/2.6	None	application	bioinformatics	Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
bracken	3.1	bracken/3.1	None	application	bioinformatics	Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
braker2	2.1.2	braker2/2.1	None	application	computational biology	BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.
braker3	3.0.8	braker3/3.0	None	application	computational biology	BRAKER3 is the latest pipeline in the BRAKER suite
breakdancer	1.4	breakdancer/1.4	None	application	computational biology	BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.
breakseq2	2.2	breakseq2/2.2	None	application	computational biology	BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants.
bsmap	2.90	bsmap/2.90	None	application	Mapping	BSMAP is a short reads mapping software for bisulfite sequencing reads.
busco	3.0.2	busco/py27/3.0	None	application	computational biology	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 selected from OrthoDB.
busco	3.0.2	busco/py35/3.0	None	application	computational biology	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 selected from OrthoDB.
busco	3.0.2	busco/py36/3.0	None	application	computational biology	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 selected from OrthoDB.
busco	4.0.6	busco/py36/4.0	None	application	computational biology	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 selected from OrthoDB.
busco	5.4.3	busco/py39/5.4	None	application	computational biology	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 selected from OrthoDB.
bwa	0.6.2	bwa/0.6	None	application	computational biology	Burrow-Wheeler Aligner for short-read alignment.
bwa	0.7.17	bwa/0.7	None	application	computational biology	Burrow-Wheeler Aligner for short-read alignment.
bwa-mem2	2.2.1	bwa-mem2/2.2	None	application	computational biology	The next version of bwa-mem.
bx-python	0.8.1	bx-python/py27/0.8	None	application	computational biology	Tools for manipulating biological data, particularly multiple sequence alignments
bx-python	0.8.1	bx-python/py35/0.8	None	application	computational biology	Tools for manipulating biological data, particularly multiple sequence alignments
bx-python	0.8.1	bx-python/py36/0.8	None	application	computational biology	Tools for manipulating biological data, particularly multiple sequence alignments
bzip2	1.0	bzip2/1.0	compiler/intel/20 None compiler/gcc/9 compiler/intel/19 compiler/intel/18 compiler/gcc/11 compiler/gcc/10	library	runtime support
bzip2	1.0.8	bzip2/1.0	compiler/pgi/20	library	runtime support
caffe	1.0	caffe/1.0	None	application	package	It is developed by the Berkeley Vision and Learning Center (BVLC) and by community contributors. Yangqing Jia created the project during his PhD at UC Berkeley. Caffe is released under the BSD 2-Clause license.
caffe-gpu	1.0	caffe-gpu/1.0	None	application	package	It is developed by the Berkeley Vision and Learning Center (BVLC) and by community contributors. Yangqing Jia created the project during his PhD at UC Berkeley. Caffe is released under the BSD 2-Clause license.
cairo	1.16.0	cairo/1.16	compiler/pgi/20 compiler/intel/20	library	runtime support
canu	1.7	canu/1.7	None	application	computational biology	Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
canu	1.8	canu/1.8	None	application	computational biology	Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
canu	2.1.1	canu/2.1	None	application	computational biology	Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
canu	2.2	canu/2.2	None	application	computational biology	Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
cap3	122107	cap3/122107	None	application	computational biology	CAP3: A DNA Sequence Assembly Program
carlsim	3.1	carlsim/3.1	None	application	computational biology	CARLsim is an efficient, easy-to-use, GPU-accelerated software framework for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail.
carlsim	4.0	carlsim/4.0	None	application	computational biology	CARLsim is an efficient, easy-to-use, GPU-accelerated software framework for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail.
carnac-lr	1.0.0	carnac-lr/1.0	None	application	computational biology	Clustering coefficient-based Acquisition of RNA Communities in Long Read
carveme	1.5.1	carveme/1.5	None	application	genomics	CarveMe is a python-based tool for genome-scale metabolic model reconstruction.
cas-offinder	2.4	cas-offinder/2.4	None	application	Biology	Cas-OFFinder is OpenCL based, ultrafast and versatile program that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases (RGEN).
cblaster	1.3.11	cblaster/1.3	None	application	computational biology	Find clustered hits from a BLAST search.
ccat	3.0	ccat/3.0	None	application	computational biology	A software package for the analysis of ChIP-seq data with negative control.
ccp4	7.0	ccp4/7.0	None	unknown	unknown
ccp4	9.0	ccp4/9.0	None	unknown	unknown
cd-hit	4.8.1	cd-hit/4.8	None	application	Bioinformatics	CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
cd-hit-auxtools	4.6.8	cd-hit-auxtools/4.6	None	application	Bioinformatics	CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. This module specifically loads the auxillary tools.
cdna-cupcake-tofu2	5.2	cdna-cupcake-tofu2/5.2	None	application	computational biology	cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.
cdo	1.9.7.1	cdo/1.9	None	application	Utilities	CLI tools to manipulate and analyse Climate and NWP model Data
cdo	2.4.0	cdo/2.4	None	application	Utilities	CLI tools to manipulate and analyse Climate and NWP model Data
cdsapi	0.6.1	cdsapi/py39/0.6	None	application	Copernicus Climate Data Store	API to access the Copernicus Climate Data Store at ECMWF
cdsapi	0.6.1	cdsapi/py310/0.6	None	application	Copernicus Climate Data Store	API to access the Copernicus Climate Data Store at ECMWF
cdsapi	0.6.1	cdsapi/py311/0.6	None	application	Copernicus Climate Data Store	API to access the Copernicus Climate Data Store at ECMWF
cdsapi	0.7.2	cdsapi/py310/0.7	None	application	Copernicus Climate Data Store	API to access the Copernicus Climate Data Store at ECMWF
cdsapi	0.7.2	cdsapi/py312/0.7	None	application	Copernicus Climate Data Store	API to access the Copernicus Climate Data Store at ECMWF
cellranger	3.0.2	cellranger/3.0	None	application	computational biology	Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
cenote-taker2	2.1.2	cenote-taker2/2.1	None	application	computational biology	Cenote-Taker2 is a pipeline for divergent virus discovery and annotation.
cenote-taker2	2020.04.01	cenote-taker2/2020.04.01	None	application	computational biology	Cenote-Taker2 is a pipeline for divergent virus discovery and annotation.
cexor	1.10	cexor/1.10	None	application	computational biology	An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates.
cgmaptools	0.1.2	cgmaptools/0.1	None	application	computational biology	Command-line Toolset for Bisulfite Sequencing Data Analysis
changeo	1.3.1	changeo/1.3	None	application	Bioinformatic	Change-O is a collection of tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin (Ig) sequences, and reconstructing germline sequences.
checkm-genome	1.0.18	checkm-genome/1.0	None	application	computational biology	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
checkm-genome	1.1.2	checkm-genome/1.1	None	application	computational biology	Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
checkm2	1.0.1	checkm2/1.0	None	application	bioinformatics	CheckM2 - Predicting the quality of metagenome-recovered bins
checkv	0.7.0	checkv/0.7	None	application	Biology	Assess the quality of metagenome-assembled viral genomes.
checkv	0.8.1	checkv/0.8	None	application	Biology	Assess the quality of metagenome-assembled viral genomes.
chemdata	1.0	chemdata/1.0	None	application	computational chemistry	Static data resources for computational chemistry (docking, etc.).
chewbbaca	2.8.4	chewbbaca/2.8	None	application	computational biology	A complete suite for gene-by-gene schema creation and strain identification.
chromosomer	0.1.4a	chromosomer/0.1.4a	None	application	Bioinformatics	A reference-assisted assembly tool for producing draft chromosome sequences.
circlator	1.5.5	circlator/1.5	None	application	Biology	circlator: a tool to circularise genome assemblies
circleator	1.0.2	circleator/1.0	None	application	computational biology	Flexible circular visualization of genome-associated data with BioPerl and SVG.
cite-seq-count	1.4.4	cite-seq-count/1.4	None	application	Bioinformatics	A python package to map reads from CITE-seq or hashing data for single cell experiments
clark	1.2	clark/1.2	None	application	computational biology
clearcut	1.0	clearcut/1.0	None	application	computational biology	Clearcut - The reference implementation for Relaxed Neighbor Joining (RNJ)
clove	0.17	clove/0.17	None	application	computational biology	CLOVE: Classification of genomic fusions into structural variation events.
clustal-omega	1.2	clustal-omega/1.2	None	application	computational biology	Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours
clustalw	2.1	clustalw/2.1	None	application	computational biology	ClustalW2 is a multiple sequence alignment tool for the alignment of DNA or protein sequences.
cmake	2.8.10.2	cmake/2.8	None	application	system	CMake is an extensible, open-source system that manages the build process
cmake	3.10.3	cmake/3.10	None	application	system	CMake is an extensible, open-source system that manages the build process
cmake	3.11.3	cmake/3.11	None	application	system	CMake is an extensible, open-source system that manages the build process
cmake	3.14.5	cmake/3.14	None	application	system	CMake is an extensible, open-source system that manages the build process
cmake	3.17.0	cmake/3.17	None	application	system	CMake is an extensible, open-source system that manages the build process
cmake	3.20.5	cmake/3.20	None	application	system	CMake is an extensible, open-source system that manages the build process
cmake	3.28.3	cmake/3.28	None	application	system	CMake is an extensible, open-source system that manages the build process
cmake	3.5.0	cmake/3.5	None	application	system	CMake is an extensible, open-source system that manages the build process
cmake	3.7.1	cmake/3.7	None	application	system	CMake is an extensible, open-source system that manages the build process
cnvcaller	0.0.2024.01.18	cnvcaller/2024.01.18	None	application	computational biology	CNVcaller is designed to detect copy number variation using sequencing data from populations.
cnvkit	0.9.10	cnvkit/0.9	None	application	bioinformatics	Copy number variant detection from high-throughput sequencing
cobra	0.17.1	cobra/py36/0.17	None	application	Biology	COBRApy is a package for constraints-based modeling of metabolic networks.
cobra	0.17.1	cobra/py37/0.17	None	application	Biology	COBRApy is a package for constraints-based modeling of metabolic networks.
cobra	0.26.3	cobra/py38/0.26	None	application	Biology	COBRApy is a package for constraints-based modeling of metabolic networks.
cobra	0.26.3	cobra/py39/0.26	None	application	Biology	COBRApy is a package for constraints-based modeling of metabolic networks.
cobra	0.26.3	cobra/py310/0.26	None	application	Biology	COBRApy is a package for constraints-based modeling of metabolic networks.
code-server	4.17.1	code-server/4.17	None	application	Development	VS Code in the browser.
code-server	4.89.1	code-server/4.89	None	application	Development	VS Code in the browser.
codonw	1.4.4	codonw/1.4	None	application	computational biology	CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage.
cogent	3.1	cogent/3.1	None	application	computational biology	Cogent is a tool for reconstructing the coding genome using high-quality full-length transcriptome sequences.
coin-or	1.8	coin-or/1.8	compiler/gcc/9	library	Open-source mixed integer linear programming solver
colony2	20230425	colony2/20230425	compiler/gcc/9 compiler/intel/18	application	computational biology
compass-cplex	0.2022.04.02	compass-cplex/2022.04.02	None	application	bioinformatics	In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes.
compiler/clang	13	compiler/clang/13	None	application	compiler
compiler/clang	17	compiler/clang/17	None	application	compiler
compiler/clang	18	compiler/clang/18	None	application	compiler
compiler/gcc	10	compiler/gcc/10	None	application	compiler
compiler/gcc	11	compiler/gcc/11	None	application	compiler
compiler/gcc	12	compiler/gcc/12	None	application	compiler
compiler/gcc	13.2	compiler/gcc/13	None	application	compiler
compiler/gcc	14.2	compiler/gcc/14	None	application	compiler
compiler/gcc	9	compiler/gcc/9	None	application	compiler
compiler/intel	18	compiler/intel/18	None	application	compiler
compiler/intel	19	compiler/intel/19	None	application	compiler
compiler/intel	20	compiler/intel/20	None	application	compiler
compiler/intel	2021.5	compiler/intel/2021	None	application	compiler
compiler/intel	2024.2	compiler/intel/2024	None	application	compiler
compiler/nvhpc	21.9	compiler/nvhpc/21.9	None	application	compiler	NVIDIA HPC SDK for Linux.
compiler/nvhpc	24.5	compiler/nvhpc/24.5	None	application	compiler	NVIDIA HPC SDK for Linux.
compiler/nvhpc	25.3	compiler/nvhpc/25.3	None	application	compiler	NVIDIA HPC SDK for Linux.
compiler/pgi	18	compiler/pgi/18	None	application	compiler
compiler/pgi	19	compiler/pgi/19	None	application	compiler
compiler/pgi	20	compiler/pgi/20	None	application	compiler
compleasm	0.2.6	compleasm/0.2	None	application	bioinformatics	Compleasm: a faster and more accurate reimplementation of BUSCO
comsol	5.4	comsol/5.4	None	application	simulation	COMSOL Multiphysics
comsol	5.5	comsol/5.5	None	application	simulation	COMSOL Multiphysics
comsol	5.6	comsol/5.6	None	application	simulation	COMSOL Multiphysics
comsol	6.0	comsol/6.0	None	application	simulation	COMSOL Multiphysics
concoct	1.1.0	concoct/1.1	None	application	Genomics	Clustering cONtigs with COverage and ComposiTion
conn	18b	conn/18b	None	application	matlab toolbox	CONN is a Matlab-based cross-platform software for the computation, display, and analysis of functional connectivity in fMRI (fcMRI).
connectome-workbench	1.3.2	connectome-workbench/1.3	None	application	neuroimaging	Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project
connectome-workbench	2.0.1	connectome-workbench/2.0	None	application	neuroimaging	Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project
consurf	1.0.0	consurf/1.0	None	application	Biology	Stand Alone version of ConSurf
conterminator	1.c74b5	conterminator/1.c74b5	None	application	computational biology	Efficient method for detecting incorrectly labeled sequences across kingdoms
convert3d	1.3.0	convert3d/1.3	None	application	utility	ITK-based image manipulation tool
coreutils	8.31	coreutils/8.31	None	application	shell tool	The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system.
corretto-jdk	11	corretto-jdk/11	None	application	system	Amazon Corretto (Java).
corretto-jdk	17	corretto-jdk/17	None	application	system	Amazon Corretto (Java).
corretto-jdk	21	corretto-jdk/21	None	application	system	Amazon Corretto (Java).
corretto-jdk	22	corretto-jdk/22	None	application	system	Amazon Corretto (Java).
corretto-jdk	8	corretto-jdk/8	None	application	system	Amazon Corretto (Java).
cosmomvpa	d43b0e7	cosmomvpa/d43b0e7	None	application	matlab toolbox	A multi-modal, multi-variate pattern analysis (MVPA) toolbox in Matlab and GNU Octave for cognitive neuroscientists.
coverm	0.6.1	coverm/0.6	None	application	computational biology	CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications
cp2k	2023.1	cp2k/2023.1	compiler/intel/20:openmpi/4.1 compiler/gcc/10:openmpi/4.1	application	quantum chemistry	Quantum chemistry and solid state physics software package
cp2k	2024.3	cp2k/2024.3	compiler/intel/20:openmpi/4.1	application	quantum chemistry	Quantum chemistry and solid state physics software package
cp2k	8.2.0	cp2k/8.2	compiler/gcc/10:openmpi/4.1	application	quantum chemistry	Quantum chemistry and solid state physics software package
cp2k	9.1	cp2k/9.1	compiler/intel/20:openmpi/4.1	application	quantum chemistry	Quantum chemistry and solid state physics software package
cp2k	9.1.0	cp2k/9.1	compiler/gcc/10:openmpi/4.1	application	quantum chemistry	Quantum chemistry and solid state physics software package
crest	1.0	crest/1.0	None	application	computational biology
crossmap	0.7.0	crossmap/0.7	None	application	bioinformatics	CrossMap is a program for convenient conversion of genome coordinates and genome annotation files between assemblies.
csaw	1.4	csaw/1.4	None	application	computational biology	Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.
cuda	10.0	cuda/10.0	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cuda	10.2	cuda/10.2	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cuda	11.0	cuda/11.0	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cuda	11.2	cuda/11.2	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cuda	11.4	cuda/11.4	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cuda	11.6	cuda/11.6	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cuda	11.8	cuda/11.8	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cuda	12.2	cuda/12.2	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cuda	12.4	cuda/12.4	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cuda	6.0	cuda/6.0	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cuda	6.5	cuda/6.5	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cuda	7.5	cuda/7.5	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cuda	8.0	cuda/8.0	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cuda	9.0	cuda/9.0	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cuda	9.1	cuda/9.1	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cuda	9.2	cuda/9.2	None	application	compiler	NVIDIA CUDA Toolkit for Linux.
cudnn	v5	cudnn/v5	None	application	compiler	NVIDIA cuDNN Toolkit for Linux.
cufflinks	2.1	cufflinks/2.1	None	application	computational biology	Transcriptome assembly and differential expression analysis for RNA-Seq.
cufflinks	2.2.1	cufflinks/2.2	None	application	computational biology	Transcriptome assembly and differential expression analysis for RNA-Seq.
curl	7.50	curl/7.50	None	application	network
curl	7.76	curl/7.76	compiler/intel/20 compiler/intel/2021 compiler/gcc/9 compiler/intel/19 compiler/gcc/10 compiler/gcc/11	application	network
cutadapt	1.13	cutadapt/1.13	None	application	NGS data	Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cutadapt	1.4	cutadapt/1.4	None	application	NGS data	Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cutadapt	2.8	cutadapt/2.8	None	application	NGS data	Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cutadapt	2.9	cutadapt/2.9	None	application	NGS data	Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cutruntools	2020.07.10	cutruntools/2020.07.10	None	application	computational biology	CUT&RUNTools is a flexible pipeline for CUT&RUN processing and footprint analysis.
cytoscape	3.10.1	cytoscape/3.10	None	unknown	unknown	Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.
cytoscape	3.6	cytoscape/3.6	None	unknown	unknown	Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.
das_tool	1.1.2	das_tool/1.1	None	application	Genomics	Recovery of genomes from metagenomes via a dereplication,aggregation and scoring strategy.
dastk	1.0.0	dastk/1.0	None	application	Bioinformatics	Differential ATAC-seq toolkit
dcm2niix	1.0.20230411	dcm2niix/1.0	None	application	neuroimaging	dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format.
deap	1.0	deap/1.0	None	application	computer science	DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas.
dedalus	2.1905	dedalus/py37/2.1905	None	application	partial differential equation	A flexible framework for solving differential equations using spectral methods.
dedalus	2.2006	dedalus/py37/2.2006	None	application	partial differential equation	A flexible framework for solving differential equations using spectral methods.
dedalus	2.2207.3	dedalus/2.2207	compiler/gcc/11:openmpi/4.1	application	partial differential equation	A flexible framework for solving differential equations using spectral methods.
dedup	0.12.8	dedup/0.12	None	application	DNA sequencing	DeDup is a tool for read deduplication in paired-end read merging
deepmd-kit	2.0.3	deepmd-kit/2.0	None	application	molecular dynamics	Deep learning package for many-body potential energy representation and molecular dynamics.
deepmd-kit	2.2.5	deepmd-kit/py39/2.2	None	application	molecular dynamics	Deep learning package for many-body potential energy representation and molecular dynamics.
deepmd-kit	2.2.5	deepmd-kit/py310/2.2	None	application	molecular dynamics	Deep learning package for many-body potential energy representation and molecular dynamics.
deepmd-kit-gpu	2.0.3	deepmd-kit-gpu/2.0	None	application	molecular dynamics	Deep learning package for many-body potential energy representation and molecular dynamics.
deepmd-kit-gpu	2.2.5	deepmd-kit-gpu/py39/2.2	None	application	molecular dynamics	Deep learning package for many-body potential energy representation and molecular dynamics.
deepmd-kit-gpu	2.2.5	deepmd-kit-gpu/py310/2.2	None	application	molecular dynamics	Deep learning package for many-body potential energy representation and molecular dynamics.
deepmriprep	0.1.0	deepmriprep/py39/0.1	None	application	computational neuroimaging	Neural network-based preprocessing of MRI data. Prepping brain images in seconds.
deeptools	2.5.4	deeptools/2.5	None	application	computational biology
deeptools	3.0.2	deeptools/3.0	None	application	computational biology
deeptools	3.5.1	deeptools/3.5	None	application	computational biology
deepvirfinder	2020.11.21	deepvirfinder/2020.11.21	None	application	metagenomics	Identifying viruses from metagenomic data by deep learning.
defiant	2019.03.02	defiant/2019.03.02	None	application	computational biology	Differential methylation, Easy, Fast, Identification and ANnoTation.
delly	0.8.3	delly/0.8	None	application	Biology	Structural variant discovery by integrated paired-end and split-read analysis
delly	0.9.1	delly/0.9	None	application	Biology	Structural variant discovery by integrated paired-end and split-read analysis
delly-omp	0.8.3	delly-omp/0.8	None	application	Biology	Structural variant discovery by integrated paired-end and split-read analysis.
demultiplex	1.2.2	demultiplex/1.2	None	application	Genomics	Demultiplex any number of FASTA or a FASTQ files based on a list of barcodes
desman	2.1	desman/2.1	None	application	computational biology	De novo Extraction of Strains from MetAgeNomes
detectron	2018.09.11	detectron/py27/2018.09.11	None	application	object detection	FAIR's research platform for object detection research, implementing popular algorithms like Mask R-CNN and RetinaNet.
detectron2	0.2.1	detectron2/py37/0.2	None	application	object detection	Detectron2 is FAIR's next-generation platform for object detection and segmentation.
dftd4	3.3.0	dftd4/3.3	compiler/intel/19 compiler/gcc/9 compiler/intel/2024 compiler/intel/20 compiler/gcc/10	application	Physics
diamond	0.9.25	diamond/0.9	None	application	Computational Biology	Accelerated BLAST compatible local sequence aligner
diamond	2.0.9	diamond/2.0	None	application	Computational Biology	Accelerated BLAST compatible local sequence aligner
diamond	2.1.9	diamond/2.1	None	application	Computational Biology	Accelerated BLAST compatible local sequence aligner
diffsplice	0.1.11	diffsplice/0.1	None	application	computational biology	DiffSplice: the Genome-Wide Detection of Differential Splicing Events with RNA-seq
dmtcp	2.0	dmtcp/2.0	None	application	Utility
dmtcp	2.3	dmtcp/2.3	None	application	Utility
dmtcp	2.4	dmtcp/2.4	None	application	Utility
dmtcp	2.5	dmtcp/2.5	None	application	Utility
dmtcp	2.6	dmtcp/2.6	compiler/intel/20 compiler/gcc/9 None compiler/gcc/10 compiler/intel/19	application	Utility
dorado	0.4.2	dorado/0.4	None	application	bioinformatics	Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
dorado	0.6.0	dorado/0.6	None	application	bioinformatics	Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
dorado	0.7.2	dorado/0.7	None	application	bioinformatics	Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
dorado-gpu	0.4.2	dorado-gpu/0.4	None	application	bioinformatics	Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
dorado-gpu	0.6.0	dorado-gpu/0.6	None	application	bioinformatics	Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
dorado-gpu	0.7.2	dorado-gpu/0.7	None	application	bioinformatics	Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
dram	1.0.6	dram/1.0	None	application	genomics	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
dram	1.2.0	dram/1.2	None	application	genomics	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
dram	1.5.0	dram/1.5	None	application	genomics	Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
drep	2.3.2	drep/2.3	None	application	Biology	De-replication of microbial genomes assembled from multiple samples
dsk	2.3.3	dsk/2.3	None	application	computational biology	DSK is a k-mer counter for reads or genomes.
dssp	4.4.7	dssp/4.4	None	application	computational biology	Application to assign secondary structure to proteins.
dtiprep	1.2	dtiprep/1.2	None	application	unknown	DTIPrep is a neuroimaging tool that performs a Study-specific Protocol based automatic pipeline for DWI/DTI quality control and preparation.
ea-utils	1.01	ea-utils/1.0	None	application	computational biology	EA Utils is a collection of command line tools for processing NextGen sequencing data. Included are fastq-stats and sam-stats which are lightweight tools that display a variety of statistics on fastq and sam files.
eccodes	2.24.2	eccodes/2.24	compiler/intel/19 compiler/intel/20 compiler/gcc/9 compiler/pgi/20 compiler/gcc/10	application	package
effector-p	2.0	effector-p/2.0	None	application	Biology	EffectorP is a machine learning method for fungal effector prediction in secretomes.
eggnog-mapper	2.1.3	eggnog-mapper/2.1	None	application	Biology	Fast genome-wide functional annotation through orthology assignment.
eigen	3.3.3	eigen/3.3	None	application	C++	C++ template library for linear algebra
eigen	3.4.0	eigen/3.4	None	application	C++	C++ template library for linear algebra
eigensoft	8.0.0	eigensoft/8.0	None	application	genomics	The EIGENSOFT package implements methods for analzing population structure and performing stratification correction
elk	8.7.10	elk/8.7	compiler/intel/20:openmpi/4.0	library	runtime support
elk	9.5.1	elk/9.5	compiler/intel/20:openmpi/4.0	library	runtime support
emacs	26.2	emacs/26.2	None	application	Utility	GNU Emacs is an extensible, customizable text editor.
emacs	27.2	emacs/27.2	None	application	Utility	GNU Emacs is an extensible, customizable text editor.
emacs	28.2	emacs/28.2	None	application	Utility	GNU Emacs is an extensible, customizable text editor.
emacs	29.3	emacs/29.3	None	application	Utility	GNU Emacs is an extensible, customizable text editor.
eman2	2022.11.06	eman2/2022.11.06	compiler/gcc/9:openmpi/4.1 compiler/gcc/10:openmpi/4.1	application	image processing	A scientific image processing software suite with a focus on CryoEM and CryoET.
emboss	6.5.7	emboss/6.5	None	application	computational biology	EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
emboss	6.6.0	emboss/6.6	None	application	computational biology	EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
emirge	0.61.1	emirge/0.61	None	application	Biology	EMIRGE reconstructs full length ribosomal genes from short read sequencing data.
ensembl-vep	104.3	ensembl-vep/104.3	None	application	Biology	The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
ensembl-vep	96.0	ensembl-vep/96.0	None	application	Biology	The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
ensembl-vep	99.2	ensembl-vep/99.2	None	application	Biology	The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
entrez-direct	10.0	entrez-direct/10.0	None	application	Entrez	Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
entrez-direct	11.0	entrez-direct/11.0	None	application	Entrez	Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
entrez-direct	13.3	entrez-direct/13.3	None	application	Entrez	Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
entrez-direct	16.2	entrez-direct/16.2	None	application	Entrez	Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
epic2	0.0.50	epic2/0.0.50	None	application	Biology	Ultraperformant Chip-Seq broad domain finder based on SICER.
epivia	1.1.2	epivia/1.1	None	application	Epigenomics	Virial Integration Analysis with epigenetic data
epoch	4.17.16	epoch/4.17	compiler/intel/20:openmpi/4.0	application	Applications
epoch	4.17.16	epoch/4.19	compiler/intel/20:openmpi/4.0	application	Applications
eqtlbma	1.3	eqtlbma/1.3	None	application	biology	Package to detect eQTLs jointly in multiple subgroups (e.g. tissues) via Bayesian Model Averaging.
erne	2.1.1	erne/2.1	None	application	computational biology	ERNE is a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads.
esmf	8.2.0	esmf/8.2	compiler/intel/19:openmpi/4.0	application	Utility
espresso	6.8	espresso/6.8	compiler/intel/20:openmpi/4.0 compiler/intel/20:openmpi/4.1	library	runtime support
espresso	7.0	espresso/7.0	compiler/intel/20:openmpi/4.1	library	runtime support
espresso	7.1	espresso/7.1	compiler/intel/20:openmpi/4.0 compiler/intel/20:openmpi/4.1	library	runtime support
espresso	7.3	espresso/7.3	compiler/intel/20:openmpi/4.0 compiler/intel/20:openmpi/4.1	library	runtime support
espresso-gpu	7.1	espresso-gpu/7.1	compiler/nvhpc/21.9:openmpi/3.1	library	runtime support
espresso-gpu	7.3	espresso-gpu/7.3	compiler/nvhpc/21.9:openmpi/3.1	library	runtime support
espresso-plumed	6.2	espresso-plumed/6.2	compiler/intel/20:openmpi/4.1	library	runtime support
ete3	3.1.1	ete3/3.1	None	application	NCBI	Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
evidencemodeler	1.1.1	evidencemodeler/1.1	None	application	computational biology	EVidence Modeler.
exomiser	7.2	exomiser/7.2	None	application	computational biology	The Exomiser is a Java program that finds potential disease-causing variants from whole-exome or whole-genome sequencing data.
exonerate	2.2.0	exonerate/2.2	None	application	computational biology	Exonerate - A generic tool for pairwise sequence comparison / alignment
exonerate	2.4.0	exonerate/2.4	None	application	computational biology	Exonerate - A generic tool for pairwise sequence comparison / alignment
expansionhunterdenovo	0.9.0	expansionhunterdenovo/0.9	None	application	computational biology	ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).
expat	2.2.9	expat/2.2	compiler/intel/20 compiler/intel/19 compiler/pgi/20 compiler/gcc/9 compiler/gcc/10	library	runtime support
export2graphlan	0.20	export2graphlan/0.20	None	application	bioinformatics	export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn.
express	1.5	express/1.5	None	application	life sciences	express - Streaming quantification for high-throughput sequencing
fair-esm	2.0.0	fair-esm/py39/2.0	None	application	evolutionary modeling	Evolutionary Scale Modeling (esm): Pretrained language models for proteins. From Facebook AI Research.
fair-esm	2.0.0	fair-esm/py310/2.0	None	application	evolutionary modeling	Evolutionary Scale Modeling (esm): Pretrained language models for proteins. From Facebook AI Research.
fair-esm-gpu	2.0.0	fair-esm-gpu/py39/2.0	None	application	evolutionary modeling	Evolutionary Scale Modeling (esm): Pretrained language models for proteins. From Facebook AI Research.
fair-esm-gpu	2.0.0	fair-esm-gpu/py310/2.0	None	application	evolutionary modeling	Evolutionary Scale Modeling (esm): Pretrained language models for proteins. From Facebook AI Research.
fargene	0.1	fargene/0.1	None	application	bioinformatics	Fragmented Antibiotic Resistance Gene iENntifiEr takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output
fastani	1.32	fastani/1.32	None	application	Biology	FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).
fastcluster	1.2.6	fastcluster/py39/1.2	None	application	machine learning	Fast hierarchical clustering routines for R and Python.
fastcluster	1.2.6	fastcluster/py310/1.2	None	application	machine learning	Fast hierarchical clustering routines for R and Python.
fastp	0.23.2	fastp/0.23	None	application	bioinformatics	A ultra-fast FASTQ preprocessor with full features (QC/adapters/trimming/filtering/splitting...)
fastq-screen	0.15.3	fastq-screen/0.15	None	application	computational biology	FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect
fastq_utils	0.25.2	fastq_utils/0.25	None	application	Genomics	Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.
fastqc	0.10.1	fastqc/0.10	None	application	computational biology	fastqc - A Quality Control application for FastQ files
fastqc	0.11.7	fastqc/0.11	None	application	computational biology	fastqc - A Quality Control application for FastQ files
fastqc	0.12.1	fastqc/0.12	None	application	computational biology	fastqc - A Quality Control application for FastQ files
fastspar	0.0.10	fastspar/0.0.10	None	application	computational biology	Rapid and scalable correlation estimation for compositional data
faststructure	1.0	faststructure/1.0	None	application	computational biology	A variational framework for inferring population structure from SNP genotype data.
fasttree	2.1.11	fasttree/2.1	None	application	computational biology	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
fastx_toolkit	0.0.14	fastx_toolkit/0.0.14	None	application	computational biology	FASTX Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
fegenie	1.0	fegenie/1.0	None	application	genomics	HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes.
feh	3.3	feh/3.3	None	application	Utility	feh is an X11 image viewer aimed mostly at console users.
feh	3.9.1	feh/3.9	None	application	Utility	feh is an X11 image viewer aimed mostly at console users.
fenics	2018.1.0	fenics/2018.1	None	application	partial differential equations	FEniCS is a collection of free software for automated, efficient solution of differential equations
fenics	2019.1.0	fenics/2019.1	compiler/gcc/10:openmpi/4.1	application	partial differential equations	FEniCS is a collection of free software for automated, efficient solution of differential equations
ffmpeg	4.3.1	ffmpeg/4.3	None	application	Utility	Cross-platform solution to record, convert and stream audio and video.
ffmpeg	4.4.1	ffmpeg/4.4	None	application	Utility	Cross-platform solution to record, convert and stream audio and video.
ffmpeg	5.1.2	ffmpeg/5.1	None	application	Utility	Cross-platform solution to record, convert and stream audio and video.
ffmpeg	6.0.0	ffmpeg/6.0	None	application	Utility	Cross-platform solution to record, convert and stream audio and video.
ffmpeg	7.1.0	ffmpeg/7.1	None	application	Utility	Cross-platform solution to record, convert and stream audio and video.
fftw3	3.3	fftw3/3.3	compiler/intel/20:openmpi/4.1 compiler/gcc/10:openmpi/4.1 compiler/gcc/9 compiler/intel/20:openmpi/4.0 compiler/intel/18:openmpi/4.0 compiler/gcc/10 compiler/pgi/20:openmpi/4.1 compiler/intel/19:openmpi/4.0 compiler/intel/19:openmpi/4.1 compiler/gcc/9:openmpi/4.1 compiler/gcc/11:openmpi/4.1 compiler/pgi/20:openmpi/4.0 compiler/intel/20 compiler/intel/19 compiler/gcc/11 compiler/intel/18 compiler/gcc/11:openmpi/4.0 compiler/intel/18:openmpi/4.1 compiler/gcc/10:openmpi/4.0 compiler/pgi/20 None compiler/gcc/9:openmpi/4.0	library	runtime support
fgbio	0.8.0	fgbio/0.8	None	application	Genomics	A set of tools for working with genomic and high throughput sequencing data, including UMIs
figtree	1.4.4	figtree/1.4	None	application	Utilities	FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures.
fiji	20220414	fiji/20220414	None	application	Image Processing	Fiji is an image processing package—a 'batteries-included' distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
filtlong	0.2.1	filtlong/0.2	None	application	Bioinformatics	Filtlong is a tool for filtering long reads. 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.
flash	1.2.11	flash/1.2	None	application	bioinformatics	Merge paired sequencing reads into single longer sequences
flash2	2.2.00	flash2/2.2	None	application	bioinformatics	Merge paired-end reads from fragments that are shorter than twice the read length
fleur	6.2	fleur/6.2	compiler/gcc/11:openmpi/4.1	application	physics	A feature-full, freely available FLAPW (full-potential linearized augmented planewave) code, based on density-functional theory.
fleur	7.0	fleur/7.0	compiler/gcc/9:openmpi/4.1	application	physics	A feature-full, freely available FLAPW (full-potential linearized augmented planewave) code, based on density-functional theory.
fleur	7.1	fleur/7.1	compiler/gcc/9:openmpi/4.0	application	physics	A feature-full, freely available FLAPW (full-potential linearized augmented planewave) code, based on density-functional theory.
flex	3.7.5	flex/2.6	None	application	Utility	General purpose parser generator converting annotated context-free grammar to a deterministic LR/GLR parser.
flye	2.8.3	flye/2.8	None	application	Bioinformatics	Fast and accurate de novo assembler for single molecule sequencing reads
flye	2.9.1	flye/2.9	None	application	Bioinformatics	Fast and accurate de novo assembler for single molecule sequencing reads
foldseek	8.ef4e960	foldseek/8.ef4e960	None	application	computational bioinformatics	Foldseek: fast and accurate protein structure search
foldseek	9.427df8a	foldseek/9.427df8a	None	application	computational bioinformatics	Foldseek: fast and accurate protein structure search
fonduer	0.8.2	fonduer/py37/0.8	None	application	knowledge base	Fonduer is a Python package and framework for building knowledge base construction (KBC) applications from richly formatted data.
fortrangis	2.5	fortrangis/2.5	compiler/gcc/9 compiler/gcc/10 compiler/intel/20 compiler/intel/19	library	runtime support
fpocket	4.2.2	fpocket/4.2	None	application	Bioinformatics	fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation.
fqtrim	0.9.7	fqtrim/0.9	None	application	computational biology	fqtrim: trimming & filtering of NGS reads.
fragpipe	20.0	fragpipe/20.0	None	application	mass spectrometry	Pipeline for comprehensive analysis of shotgun proteomics data
fragpipe	22.0	fragpipe/22.0	None	application	mass spectrometry	Pipeline for comprehensive analysis of shotgun proteomics data
freebayes	1.2.0	freebayes/1.2	None	application	Biology	Bayesian haplotype-based polymorphism discovery and genotyping
freebayes	1.3.7	freebayes/1.3	None	application	Biology	Bayesian haplotype-based polymorphism discovery and genotyping
freecad	0.20.1	freecad/0.20	None	application	3D modeling	FreeCAD is a parametric 3D modeler made primarily to design real-life objects of any size.
freesurfer	5.3.0	freesurfer/5.3	None	application	computational neuroimaging	An open source software suite for processing and analyzing (human) brain MRI images.
freesurfer	6.0.1	freesurfer/6.0	None	application	computational neuroimaging	An open source software suite for processing and analyzing (human) brain MRI images.
freesurfer	7.1.1	freesurfer/7.1	None	application	computational neuroimaging	An open source software suite for processing and analyzing (human) brain MRI images.
freesurfer	7.2.0	freesurfer/7.2	None	application	computational neuroimaging	An open source software suite for processing and analyzing (human) brain MRI images.
freesurfer	7.4.1	freesurfer/7.4	None	application	computational neuroimaging	An open source software suite for processing and analyzing (human) brain MRI images.
freetype	2.10.0	freetype/2.10	compiler/pgi/20 compiler/intel/20	library	runtime support
fsl	6.0.6	fsl/6.0	None	application	computational neuroimaging	FMRIB Software Library
fusioncatcher	1.33	fusioncatcher/1.33	None	application	computational biology	Finder of Somatic Fusion Genes in RNA-seq data.
gamess	20210930R2	gamess/20210930R2	compiler/intel/19:openmpi/4.0 compiler/intel/2021:intel-mpi/2021	library	runtime support
gamess-omp	20210930R2	gamess-omp/20210930R2	compiler/intel/19:openmpi/4.0	library	runtime support
gap	4.11.0	gap/4.11	None	application	Mathematics	GAP - Groups, Algorithms, Programming, a System for Computational Discrete Algebra
gapfiller	2.1.1	gapfiller/2.1	None	application	computational biology	GapFiller is a seed-and-extend local assembler to fill the gap within paired reads.
gat	1.3.6	gat/1.3	None	application	Biology	Genomic Association Tester
gatk	3.4-46	gatk/3.4	None	application	computational biology	The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
gatk	3.7	gatk/3.7	None	application	computational biology	The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
gatk4	4.0.4.0	gatk4/4.0	None	application	computational biology	GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.
gatk4	4.1.8.1	gatk4/4.1	None	application	computational biology	GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.
gatk4	4.2.4.1	gatk4/4.2	None	application	computational biology	GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.
gatk4	4.3.0.0	gatk4/4.3	None	application	computational biology	GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.
gatk4	4.4.0.0	gatk4/4.4	None	application	computational biology	GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.
gatk4	4.6.2.0	gatk4/4.6	None	application	computational biology	GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.
gaussian	09 RevD	gaussian/09/RevD	None	application	Chemistry
gaussian	09 RevE	gaussian/09/RevE	None	application	Chemistry
gaussian	16 RevA	gaussian/16/RevA	None	application	Chemistry
gaussian	16 RevC01	gaussian/16/RevC01	None	application	Chemistry
gbmunge	2018.07.06	gbmunge/2018.07.06	None	application	computational biology	Munge GenBank files into FASTA and tab-separated metadata.
gcprofile	1.0	gcprofile/1.0	None	application	computational biology	GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences
gcta	1.94.1	gcta/1.94	None	application	computational biology	GCTA (Genome-wide Complex Trait Analysis) estimates the proportion of phenotypic variance explained by all genome-wide SNPs for complex traits.
gdal	3.4	gdal/3.4	compiler/intel/19 compiler/gcc/9 compiler/intel/20 compiler/gcc/10	library	runtime support
gdcclient	1.3.0	gdcclient/1.3	None	application	genomics	GDC provides a standard client-based mechanism in support of high performance data downloads and submission.
gdcclient	1.4.0	gdcclient/1.4	None	application	genomics	GDC provides a standard client-based mechanism in support of high performance data downloads and submission.
gdcclient	1.6.1	gdcclient/1.6	None	application	genomics	GDC provides a standard client-based mechanism in support of high performance data downloads and submission.
gem	2.7	gem/2.7	None	application	computational biology	GEM: High resolution peak calling and motif discovery for ChIP-seq and ChIP-exo data.
gemma	0.98.1	gemma/0.98	None	application	computational biology	Linear mixed models (LMMs) for genome-wide association (GWA)
gemoma	1.9	gemoma/1.9	None	application	Genome Analysis	Gene Model Mapper (GeMoMa) is a homology-based gene prediction program.
genemark-es	2.3f	genemark-es/2.3f	None	application	computational biology	GeneMark-ES.
genemarks	2.5p	genemarks/2.5p	None	application	computational biology	GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
genemarks	4.3	genemarks/4.3	None	application	computational biology	GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
genodiver	2018.11.12	genodiver/2018.11.12	None	application	biology	Geno-Diver is a complex animal genetic simulation tool that is able to simulate quantitative and/or fitness characters.
genometester4	4.0	genometester4/4.0	None	application	Bioinformatics	A toolkit for performing set operations - union, intersection and complement - on k-mer lists.
genometools/py27	1.5.10	genometools/py27/1.5	None	application	Bioinformatics	GenomeTools genome analysis system.
genometools/py35	1.5.10	genometools/py35/1.5	None	application	Bioinformatics	GenomeTools genome analysis system.
genometools/py36	1.5.10	genometools/py36/1.5	None	application	Bioinformatics	GenomeTools genome analysis system.
genozip	14.0.21	genozip/14.0	None	application	computational biology	Compressor for genomic files (FASTQ, BAM, VCF, FASTA and more), up to 5x better than gzip and faster too
gensim	3.8.0	gensim/py27/3.8	None	application	Machine learning	Topic Modelling for Humans
gensim	3.8.0	gensim/py36/3.8	None	application	Machine learning	Topic Modelling for Humans
gensim	3.8.0	gensim/py37/3.8	None	application	Machine learning	Topic Modelling for Humans
geodata	1.0	geodata/1.0	None	application	geo models	Static data resources for geo data.
geoparse	1.0.5	geoparse/1.0	None	application	Bioinformatics	Python library to access Gene Expression Omnibus Database (GEO)
geos	3.8	geos/3.8	compiler/gcc/10 compiler/gcc/9 compiler/intel/19 compiler/pgi/20 compiler/intel/20	library	runtime support
getorganelle	1.7.7.1	getorganelle/1.7	None	application	bioinformatics	Get organelle genomes from genome skimming data
gffcompare	0.10.6	gffcompare/0.10	None	application	Annotation	GffCompare by Geo Pertea
gffread	0.12.7	gffread/0.12	None	application	bioinformatics	GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.
gflags	2.1	gflags/2.1	None	library	unknown	Online documentation available at: https://gflags.github.io/gflags/
ghostscript	9.20	ghostscript/9.20	None	library	runtime support	An interpreter for the PostScript language and for PDF.
ghostscript	9.22	ghostscript/9.22	None	library	runtime support	An interpreter for the PostScript language and for PDF.
gistic2	2.0.23	gistic2/2.0	None	application	Biology	GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.
git	2.17.0	git/2.17	None	library	tools	distributed version control system
git	2.22.0	git/2.22	None	library	tools	distributed version control system
git	2.29.2	git/2.29	None	library	tools	distributed version control system
git	2.30.9	git/2.30	None	library	tools	distributed version control system
git	2.35.8	git/2.35	None	library	tools	distributed version control system
git	2.39.3	git/2.39	None	library	tools	distributed version control system
git	2.40.1	git/2.40	None	library	tools	distributed version control system
git	2.7.4	git/2.7	None	library	tools	distributed version control system
globalarrays	5.8.2	globalarrays/5.8	compiler/gcc/9:openmpi/4.1 compiler/gcc/10:openmpi/4.1 compiler/intel/19:openmpi/4.1 compiler/gcc/11:openmpi/4.1 compiler/intel/20:openmpi/4.1 compiler/intel/2021:openmpi/4.1	library	runtime support
globus-cli	1.10.1	globus-cli/1.10	None	application	tool	Globus CLI
globus-cli	1.13.0	globus-cli/1.13	None	application	tool	Globus CLI
globus-cli	1.2.0	globus-cli/1.2	None	application	tool	Globus CLI
globus-cli	2.0.0	globus-cli/2.0	None	application	tool	Globus CLI
globus-cli	3.18.0	globus-cli/3.0	None	application	tool	Globus CLI
glog	0.3.3	glog/0.3	None	application	Utility
glpk	4.61	glpk/4.61	None	application	mathematics	The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
gmap	2015.12.31	gmap/2015.12.31	None	application	computational biology	GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmap	2017.05.08	gmap/2017.05.08	None	application	computational biology	GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmap	2018.03.25	gmap/2018.03.25	None	application	computational biology	GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmap	2020.04.08	gmap/2020.04.08	None	application	computational biology	GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmap	2021.08.25	gmap/2021.08.25	None	application	computational biology	GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmap	2023.10.10	gmap/2023.10.10	None	application	computational biology	GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmcloser	1.6.2	gmcloser/1.6	None	application	computational biology	GMcloser fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads.
gmp	6.2.1	gmp/6.2	compiler/gcc/9 compiler/pgi/20 compiler/intel/20 compiler/intel/19 compiler/gcc/10	library	runtime support	GNU MP is a library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
gmx_mmpbsa	1.6.3	gmx_mmpbsa/1.6	compiler/gcc/11:openmpi/4.1	application	computational chemistry	gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
gnu-parallel	20180522	gnu-parallel/20180522	None	application	Shell tool	GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
gnu-parallel	20220722	gnu-parallel/20220722	None	application	Shell tool	GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
gnuplot	4.6.0	gnuplot/4.6	None	application	unknown	Gnuplot, plotting from command line
gnuplot	5.2.3	gnuplot/5.2	None	application	unknown	Gnuplot, plotting from command line
gnuplot	5.4.1	gnuplot/5.4	None	application	unknown	Gnuplot, plotting from command line
google-cloud-sdk	350.0.0	google-cloud-sdk/350	None	application	Utility	Command-line interface for Google Cloud Platform products and services
google-cloud-sdk	440.0.0	google-cloud-sdk/440	None	application	Utility	Command-line interface for Google Cloud Platform products and services
gradle	3.3	gradle/3.3	None	application	Utility	Gradle - an open-source build-automation system
gradle	5.6	gradle/5.6	None	application	Utility	Gradle - an open-source build-automation system
gradle	7.1.0	gradle/7.1	None	application	Utility	Gradle - an open-source build-automation system
gramalign	3.0	gramalign/3.0	None	application	computational biology	GramAlign is a time-efficient progressive Multiple Sequence Alignment (MSA) algorithm.
gramcluster	1.3	gramcluster/1.3	None	application	computational biology	GramCluster is a fast and accurate progressive clustering algorithm that relies on a grammar-based sequence distance and is particularly useful in clustering large datasets.
gramdist	1.0	gramdist/1.0	None	application	computational biology	GramDist is a utility for generating dissimilarity matrices using the relative complexity measure, a computationally efficient and alignment free evolutionary distance metric.
graphlan	1.0.0	graphlan/1.0	None	application	computational biology	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
graphlan	1.1.2	graphlan/1.1	None	application	computational biology	GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
graphviz	2.38.0	graphviz/2.38	None	application	Visualization	Open Source graph visualization software.
graphviz	2.40.1	graphviz/2.40	None	application	Visualization	Open Source graph visualization software.
graphviz	4.0.0	graphviz/4.0	None	application	Visualization	Open Source graph visualization software.
grib-api	1.21.0	grib-api/1.21	compiler/intel/20 compiler/pgi/20	library	runtime support
gromacs	2022.3	gromacs/2022.3	compiler/gcc/10:openmpi/4.1	application	computational biology	GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
gromacs	2023	gromacs/2023	compiler/gcc/10:openmpi/4.1	application	computational biology	GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
gromacs	2024.1	gromacs/2024.1	compiler/gcc/11:openmpi/4.1	application	computational biology	GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
gromacs-gpu	2021.1	gromacs-gpu/2021.1	compiler/gcc/9	application	computational biology	GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
gromacs-gpu	2022.3	gromacs-gpu/2022.3	compiler/gcc/10	application	computational biology	GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
gromacs-gpu	2023	gromacs-gpu/2023	compiler/gcc/10 compiler/gcc/10:openmpi/4.1	application	computational biology	GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
gromacs-gpu	2024.1	gromacs-gpu/2024.1	compiler/gcc/11 compiler/gcc/11:openmpi/4.1	application	computational biology	GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
groopm	0.3.4	groopm/0.3	None	application	bioinformatics	Metagenomic binning suite
gstreamer	1.20.3	gstreamer/1.20	None	application	Library for constructing graphs of media-handling components	Library for constructing graphs of media-handling components
gstreamer	1.22.5	gstreamer/1.22	None	application	Library for constructing graphs of media-handling components	Library for constructing graphs of media-handling components
gsufsort	2023.10.20	gsufsort/2023.10.20	None	application	bioinformatics	Building suffix arrays, LCP-arrays and BWTs for string collections.
gsutil	350.0.0	gsutil/4.65	None	application	Utility	Command-line interface for Google Cloud Platform products and services
gsutil	440.0.0	gsutil/5.25	None	application	Utility	Command-line interface for Google Cloud Platform products and services
gtdbtk	0.1.3	gtdbtk/0.1	None	application	computational biology	A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
gtdbtk	1.3.0	gtdbtk/1.3	None	application	computational biology	A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
gtdbtk	1.5.0	gtdbtk/1.5	None	application	computational biology	A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
gtdbtk	2.4.0	gtdbtk/2.4	None	application	computational biology	A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
gubbins	2.3.4	gubbins/2.3	None	application	Biology	Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
gubbins	3.1.6	gubbins/3.1	None	application	Biology	Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
guppy	6.2.1	guppy/6.2	None	application	Bioinformatics	Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms, and several bioinformatic post-processing features.
guppy	6.3.4	guppy/6.3	None	application	Bioinformatics	Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms, and several bioinformatic post-processing features.
guppy	6.5.7	guppy/6.5	None	application	Bioinformatics	Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms, and several bioinformatic post-processing features.
guppy-gpu	6.2.1	guppy-gpu/6.2	None	application	Bioinformatics	Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms, and several bioinformatic post-processing features.
guppy-gpu	6.3.4	guppy-gpu/6.3	None	application	Bioinformatics	Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms, and several bioinformatic post-processing features.
guppy-gpu	6.5.7	guppy-gpu/6.5	None	application	Bioinformatics	Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms, and several bioinformatic post-processing features.
gurobi	10.0.2	gurobi/py39/10.0	None	application	Mathematics	The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi	10.0.2	gurobi/py310/10.0	None	application	Mathematics	The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi	11.0.0	gurobi/py39/11.0	None	application	Mathematics	The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi	11.0.0	gurobi/py310/11.0	None	application	Mathematics	The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi	12.0.1	gurobi/py310/12.0	None	application	Mathematics	The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi	12.0.1	gurobi/py311/12.0	None	application	Mathematics	The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi	9.0.3	gurobi/py36/9.0	None	application	Mathematics	The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi	9.0.3	gurobi/py37/9.0	None	application	Mathematics	The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi	9.5.1	gurobi/py38/9.5	None	application	Mathematics	The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi	9.5.1	gurobi/py39/9.5	None	application	Mathematics	The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi-python	8.1.0	gurobi-python/py27/8.1	None	application	Mathematics	The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi-python	8.1.0	gurobi-python/py35/8.1	None	application	Mathematics	The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi-python	8.1.0	gurobi-python/py36/8.1	None	application	Mathematics	The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
halla	0.8.17	halla/0.8	None	application	computational biology	HAllA: Hierarchically All-against-All Association Testing.
hapcut2	1.3.4	hapcut2/py311/1.3	None	application	computational biology	Tools for haplotype assembly from sequence data
hapflk	1.3.0	hapflk/1.3	None	application	package	hapflk is a software implementing the hapFLK [1] and FLK [2] tests for the detection of selection signatures based on multiple population genotyping data.
hapsolo	2021.10.09	hapsolo/2021.10.09	None	application	computational biology	An optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding.
haptools	0.4.0	haptools/0.4	None	application	bioinformatics	Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis
haskell-platform	8.2.1	haskell-platform/8.2.1	None	application	Utilities	The Haskell Platform is a collection of software packages, tools and libraries that create a common platform for using and developing applications in Haskell..
haslr	0.8a1	haslr/0.8a1	None	application	genomics	A fast tool for hybrid genome assembly of long and short reads
hdf-eos2	2.20	hdf-eos2/2.20	compiler/gcc/9 compiler/gcc/10 compiler/pgi/20 compiler/intel/20 compiler/intel/19	library	runtime support
hdf4	4.2.15	hdf4/4.2	compiler/intel/20 compiler/gcc/10 compiler/gcc/9 compiler/intel/19 compiler/pgi/20	library	runtime support
hdf5	1.12	hdf5/1.12	compiler/gcc/10 compiler/gcc/9 compiler/intel/19 compiler/pgi/20 compiler/gcc/11 compiler/intel/18 compiler/intel/20	library	runtime support
hdf5	1.14.6	hdf5/1.14	compiler/intel/19 compiler/gcc/11	library	runtime support
hdf5	1.8	hdf5/1.8	None compiler/intel/18 compiler/gcc/9	library	runtime support
hiddendomains	2.3	hiddendomains/2.3	None	application	chip-seq	hiddenDomains is a suite of programs used to identify significant enrichment of ChIP-seq reads that span large domains.
hifiasm	0.19.8	hifiasm/0.19	None	application	computational biology	Haplotype-resolved assembler for accurate Hifi reads
hisat2	2.0.5	hisat2/2.0	None	application	computational biology	graph-based alignment of next generation sequencing reads to a population of genomes
hisat2	2.1.0	hisat2/2.1	None	application	computational biology	graph-based alignment of next generation sequencing reads to a population of genomes
hisat2	2.2.1	hisat2/2.2	None	application	computational biology	graph-based alignment of next generation sequencing reads to a population of genomes
hmmer	3.3.1	hmmer/3.3	compiler/gcc/11:openmpi/4.1 compiler/gcc/9:openmpi/4.0	application	computational biology	HMMER biosequence analysis using profile hidden Markov models
hmmer	3.4	hmmer/3.4	compiler/gcc/11:openmpi/4.1	application	computational biology	HMMER biosequence analysis using profile hidden Markov models
homer	4.11	homer/4.11	None	application	computational biology	Software for motif discovery and next generation sequencing analysis
hotspot3d	0.6.0	hotspot3d/0.6	None	application	bioinformatics	This 3D proximity tool can be used to identify mutation hotspots from linear protein sequence and correlate the hotspots with known or potentially interacting domains, mutations, or drugs. Mutation-mutation and mutation-drug clusters can also be identified and viewed.
htseq	0.11.2	htseq/py27/0.11	None	application	computational biology	HTSeq - Analysing high-throughput sequencing data with Python
htseq	0.11.2	htseq/py36/0.11	None	application	computational biology	HTSeq - Analysing high-throughput sequencing data with Python
htseq	0.11.2	htseq/py37/0.11	None	application	computational biology	HTSeq - Analysing high-throughput sequencing data with Python
htseq	0.13.5	htseq/py36/0.13	None	application	computational biology	HTSeq - Analysing high-throughput sequencing data with Python
htseq	0.13.5	htseq/py39/0.13	None	application	computational biology	HTSeq - Analysing high-throughput sequencing data with Python
htseq	0.5.4p5	htseq/0.5.4p5	None	application	computational biology	HTSeq - Analysing high-throughput sequencing data with Python
htseq	0.6.1p1	htseq/0.6.1p1	None	application	computational biology	HTSeq - Analysing high-throughput sequencing data with Python
htseq	0.9.1	htseq/0.9	None	application	computational biology	HTSeq - Analysing high-throughput sequencing data with Python
htseq	2.0.5	htseq/py39/2.0	None	application	computational biology	HTSeq - Analysing high-throughput sequencing data with Python
htseq	2.0.5	htseq/py310/2.0	None	application	computational biology	HTSeq - Analysing high-throughput sequencing data with Python
htslib	1.12.2	htslib/1.12	compiler/gcc/10 compiler/intel/19 compiler/intel/20 compiler/gcc/9	application	computational biology	HTSlib is an implementation of a unified C library for accessing common file formats.
htslib	1.3.2	htslib/1.3	None	application	computational biology	HTSlib is an implementation of a unified C library for accessing common file formats.
htslib	1.7	htslib/1.7	None	application	computational biology	HTSlib is an implementation of a unified C library for accessing common file formats.
htstream	e919d21	htstream/e919d21	None	application	Bioinformatics	A toolset for high throughput sequence analysis using a streaming approach facilitated by Linux pipes.
humann	3.0.0	humann/3.0	None	application	computational biology	HUMAnN 3 is the next iteration of HUMAnN, the HMP Unified Metabolic Analysis Network.
humann	3.1.1	humann/3.1	None	application	computational biology	HUMAnN 3 is the next iteration of HUMAnN, the HMP Unified Metabolic Analysis Network.
humann	3.6	humann/3.6	None	application	computational biology	HUMAnN 3 is the next iteration of HUMAnN, the HMP Unified Metabolic Analysis Network.
humann	3.9	humann/3.9	None	application	computational biology	HUMAnN 3 is the next iteration of HUMAnN, the HMP Unified Metabolic Analysis Network.
humann2	0.11.2	humann2/0.11	None	application	computational biology	HUMAnN2 is the HMP Unified Metabolic Analysis Network 2
humann2	0.9.9	humann2/0.9	None	application	computational biology	HUMAnN2 is the HMP Unified Metabolic Analysis Network 2
humann2	2.8.1	humann2/2.8	None	application	computational biology	HUMAnN2 is the HMP Unified Metabolic Analysis Network 2
hypre	2.32	hypre/2.32	compiler/gcc/10:openmpi/4.0	application	software library
i-pi	2.4.0	i-pi/py39/2.4	None	application	molecular dynamics	i-PI: a universal force engine
ibamr	0.15.0	ibamr/0.15	compiler/gcc/10:openmpi/4.0	library	runtime support
ibdseq	r1206	ibdseq/r1206	None	application	Bioinformatics	IBDseq is a method for detecting identity by descent (IBD) segments in sequence data
ibm-ilog-cplex	12.10	ibm-ilog-cplex/12.10	None	application	iIBM ILOG CPLEX Optimization Studio
ibm-ilog-cplex	20.10	ibm-ilog-cplex/20.10	None	application	iIBM ILOG CPLEX Optimization Studio
ibm-ilog-cplex	22.1.0	ibm-ilog-cplex/22.1.0	None	application	iIBM ILOG CPLEX Optimization Studio
icount	2.0.0	icount/py36/2.0	None	application	Bioinformatics	Computational pipeline for analysis of iCLIP data
icount	2.0.0	icount/py37/2.0	None	application	Bioinformatics	Computational pipeline for analysis of iCLIP data
idba	1.1.3	idba/1.1	None	application	computational biology	IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics.
idr	2.0	idr/2.0	None	application	computational biology	The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.
igs-portal-client	1.4.4	igs-portal-client/1.4	None	application	System	Python-based client for downloading data made available through portals powered by the GDC-based portal system.
igvtools	2.14.1	igvtools/2.14	None	application	genomics	Command line tools for IGV
igvtools	2.16.2	igvtools/2.16	None	application	genomics	Command line tools for IGV
igvtools	2.5.3	igvtools/2.5	None	application	genomics	Command line tools for IGV
ilastik	1.3.3post3	ilastik/1.3	None	application	Image Processing	ilastik is a gui driven open source interactive image classification, segmentation and analysis tool that uses machine learning.
ilastik	1.4.0.post1	ilastik/1.4	None	application	Image Processing	ilastik is a gui driven open source interactive image classification, segmentation and analysis tool that uses machine learning.
ilastik-gpu	1.4.0.post1	ilastik-gpu/1.4	None	application	Image Processing	ilastik is a gui driven open source interactive image classification, segmentation and analysis tool that uses machine learning.
ima3	1.0	ima3/1.0	None	application	Phylogeny	IMa3 provides for estimation of the posterior probability of the population phylogenetic topology by using a new kind of data augmentation called a 'hidden genealogy'.
imagemagick	7.0.8_10	imagemagick/7.0	None	application	bitmap	Software suite to create, edit, compose, or convert bitmap images.
imagemagick	7.1.0_2	imagemagick/7.1	None	application	bitmap	Software suite to create, edit, compose, or convert bitmap images.
imbalanced-learn-gpu	0.4.3	imbalanced-learn-gpu/py36/0.4	None	application	Machine Learning	Python module to balance data set using under- and over-sampling
imbalanced-learn-gpu	0.4.3	imbalanced-learn-gpu/py37/0.4	None	application	Machine Learning	Python module to balance data set using under- and over-sampling
impute2	2.3.2	impute2/2.3	None	application	computational biology	IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes.
instrain	1.3.7	instrain/1.3	None	application	bioinformatics	Calculation of strain-level metrics
intel-mkl	12	intel-mkl/12	None	library	tools	Numerical library, contains blas/lapack
intel-mkl	13	intel-mkl/13	None	library	tools	Numerical library, contains blas/lapack
intel-mkl	15	intel-mkl/15	None	library	tools	Numerical library, contains blas/lapack
intel-mkl	16	intel-mkl/16	None	library	tools	Numerical library, contains blas/lapack
intel-mkl	18	intel-mkl/18	None	library	tools	Numerical library, contains blas/lapack
intel-mkl	19	intel-mkl/19	None	library	tools	Numerical library, contains blas/lapack
intel-mkl	20	intel-mkl/20	None	library	tools	Numerical library, contains blas/lapack
intel-mkl	2021.1	intel-mkl/2021.1	None	library	tools	Numerical library, contains blas/lapack
intel-mkl	2022.0	intel-mkl/2022.0	None	library	tools	Numerical library, contains blas/lapack
intel-mkl	2024.2	intel-mkl/2024.2	None	library	tools	Numerical library, contains blas/lapack
intel-mpi	18	intel-mpi/18	compiler/intel/18	library	runtime support
intel-mpi	19	intel-mpi/19	compiler/intel/19	library	runtime support
intel-mpi	2021	intel-mpi/2021	compiler/intel/2021	library	runtime support
intel-tbb	2021.13	intel-tbb/2021.13	None	library	runtime support
intel-tbb	2021.2	intel-tbb/2021.2	None	library	runtime support
intel-tbb	2021.5	intel-tbb/2021.5	None	library	runtime support
interproscan	5.52-86.0	interproscan/5.52	None	application	computational biology	Scans a range of protein signatures against your sequences and provides protein functional analysis.
interproscan	5.63-95.0	interproscan/5.63	None	application	computational biology	Scans a range of protein signatures against your sequences and provides protein functional analysis.
interproscan	5.69-101.0	interproscan/5.69	None	application	computational biology	Scans a range of protein signatures against your sequences and provides protein functional analysis.
interproscan	5.8-49.0	interproscan/5.8	None	application	computational biology	Scans a range of protein signatures against your sequences and provides protein functional analysis.
ipr-support	1.0	ipr-support/1.0	None	application	computational biology	Support environment containing a few small libraries for InterProScan. Not useful as a stand-alone environment.
iqtree	1.6.7	iqtree/1.6	None	application	computational biology	IQ-TREE creates phylogenetic trees under maximum likelihood with emphasis on speed and accuracy.
iqtree	2.2.2.7	iqtree/2.2	None	application	computational biology	IQ-TREE creates phylogenetic trees under maximum likelihood with emphasis on speed and accuracy.
iqtree	2.3.4	iqtree/2.3	None	application	computational biology	IQ-TREE creates phylogenetic trees under maximum likelihood with emphasis on speed and accuracy.
irods	4.1	irods/4.1	None	application	unknown	The integrated Rule-Oriented Data System (iRODS) is open source data management software used by research organizations and government agencies worldwide. This module includes the icommands client programs only.
irods	4.2	irods/4.2	None	application	unknown	The integrated Rule-Oriented Data System (iRODS) is open source data management software used by research organizations and government agencies worldwide. This module includes the icommands client programs only.
irods	4.3	irods/4.3	None	application	unknown	The integrated Rule-Oriented Data System (iRODS) is open source data management software used by research organizations and government agencies worldwide. This module includes the icommands client programs only.
itk	5.2.0	itk/py37/5.2	None	application	Utility	ITK is an open-source toolkit for multidimensional image analysis
itk	5.2.0	itk/py38/5.2	None	application	Utility	ITK is an open-source toolkit for multidimensional image analysis
itk	5.2.0	itk/py39/5.2	None	application	Utility	ITK is an open-source toolkit for multidimensional image analysis
ivar	1.4.2	ivar/1.4	None	application	computational biology	iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
jags	4.3	jags/4.3	compiler/intel/2021 compiler/gcc/11	application	mathematics	JAGS is Just Another Gibbs Sampler.
jamm	1.0.7r2	jamm/1.0.7r2	None	application	computational biology	JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately.
jasper	1.9	jasper/1.9	compiler/pgi/20	library	runtime support	A reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
jasper	1.900.22	jasper/1.900.22	compiler/pgi/20	library	runtime support	A reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
jasper	2.0	jasper/2.0	compiler/gcc/10 compiler/pgi/20 compiler/gcc/9 compiler/intel/19 compiler/intel/20	library	runtime support	A reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
jasper	4.0.0	jasper/4.0	None	library	runtime support	A reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
java	1.6	java/1.6	None	application	system	OpenJDK (Java).
java	1.7	java/1.7	None	application	system	OpenJDK (Java).
java	1.8	java/1.8	None	application	system	OpenJDK (Java).
java	11	java/11	None	application	system	OpenJDK (Java).
java	12	java/12	None	application	system	OpenJDK (Java).
java	17	java/17	None	application	system	OpenJDK (Java).
java	19	java/19	None	application	system	OpenJDK (Java).
jellyfish	2.2.0	jellyfish/2.2	None	application	Biology	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence
jellyfish	2.3.0	jellyfish/2.3	None	application	Biology	Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence
jmosaics	1.10	jmosaics/1.10	None	application	computational biology	Joint analysis of multiple ChIP-Seq data sets.
jpeg	9e	jpeg/9e	compiler/pgi/20 compiler/intel/19 compiler/gcc/9 compiler/gcc/10 compiler/intel/20 compiler/gcc/11	library	runtime support
jq	1.6	jq/1.6	None	application	Utility	A command-line JSON processor.
juicer	1.6	juicer/1.6	None	application	computational biology	A One-Click System for Analyzing Loop-Resolution Hi-C Experiments.
julia	0.6.2	julia/0.6	None	application	Language	A high-performance dynamic programming language for data science
julia	1.0	julia/1.0	None	application	Language	A high-performance dynamic programming language for data science
julia	1.1.1	julia/1.1	None	application	Language	A high-performance dynamic programming language for data science
julia	1.10.2	julia/1.10	None	application	Language	A high-performance dynamic programming language for data science
julia	1.11.4	julia/1.11	None	application	Language	A high-performance dynamic programming language for data science
julia	1.6.1	julia/1.6	None	application	Language	A high-performance dynamic programming language for data science
julia	1.7.2	julia/1.7	None	application	Language	A high-performance dynamic programming language for data science
julia	1.9.2	julia/1.9	None	application	Language	A high-performance dynamic programming language for data science
jupyter-book	0.15.1	jupyter-book/0.15	None	application	Publishing	Jupyter Book: Create an online book with Jupyter Notebooks
justorthologs	0.0.20190308	justorthologs/0.0.20190308	None	application	Biology	JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm.
jvarkit	2024.04.20	jvarkit/2024.04.20	None	application	bioinformatics Java	Java utilities for Bioinformatics.
jvarkit-msa2vcf	1.0	jvarkit-msa2vcf/1.0	None	application	computational biology	Getting a VCF file from a CLUSTAW or a FASTA alignment.
jvarkit-sam2tsv	1.0	jvarkit-sam2tsv/1.0	None	application	computational biology	Prints the SAM alignments as a TAB delimited file.
jvarkit-vcf2bam	2018.04.05	jvarkit-vcf2bam/2018.04.05	None	application	computational biology	Converts VCF to BAM files
jwt-cli	3.3.0	jwt-cli/3.3	None	application	json	A super fast CLI tool to decode and encode JWTs built in Rust.
kaiju	1.10.0	kaiju/1.10	None	application	Bioinformatics	Fast and sensitive taxonomic classification for metagenomics
kaiju	1.7.3	kaiju/1.7	None	application	Bioinformatics	Fast and sensitive taxonomic classification for metagenomics
kaiju	1.8.2	kaiju/1.8	None	application	Bioinformatics	Fast and sensitive taxonomic classification for metagenomics
kalign	2.0	kalign/2.0	None	application	computational biology	Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences.
kalign	2.03	kalign/2.03	None	application	computational biology	Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences.
kallisto	0.46.2	kallisto/0.46	None	application	computational biology	Kallisto is a program for quantifying abundances of transcripts from bulk and single-cell 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.
kat	2.4.0	kat/2.4	None	application	bioinformatics	KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts
keras	2.2.4	keras/py27/2.2	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
keras	2.2.4	keras/py36/2.2	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
keras	2.3.1	keras/py27/2.3	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
keras	2.3.1	keras/py36/2.3	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
keras	2.4.3	keras/py37/2.4	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
keras	2.4.3	keras/py38/2.4	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
keras	2.6.0	keras/py38/2.6	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
keras	2.6.0	keras/py39/2.6	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
keras-gpu	2.2.4	keras-gpu/py27/2.2	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
keras-gpu	2.2.4	keras-gpu/py36/2.2	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
keras-gpu	2.3.1	keras-gpu/py27/2.3	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
keras-gpu	2.3.1	keras-gpu/py36/2.3	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
keras-gpu	2.4.3	keras-gpu/py37/2.4	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
keras-gpu	2.4.3	keras-gpu/py38/2.4	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
keras-gpu	2.6.0	keras-gpu/py38/2.6	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
keras-gpu	2.6.0	keras-gpu/py39/2.6	None	application	machine learning	Deep Learning Library for Theano and TensorFlow
khmer	2.0	khmer/2.0	None	application	computational biology	Khmer is tools for in-memory nucleotide sequence k-mer counting, filtering, graph traversal and more.
kmc	3.1.1	kmc/3.1	None	application	computational biology	Tools for efficient k-mer counting and filtering of reads based on k-mer content
kmc	3.2.4	kmc/3.2	None	application	computational biology	Tools for efficient k-mer counting and filtering of reads based on k-mer content
kneaddata	0.10.0	kneaddata/0.10	None	application	computational biology	KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
kneaddata	0.12.0	kneaddata/0.12	None	application	computational biology	KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
kneaddata	0.7.2	kneaddata/0.7	None	application	computational biology	KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
kraken	1.0	kraken/1.0	None	application	computational biology	Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
kraken2	2.0.8-beta	kraken2/2.0.8-beta	None	application	Bioinformatics	Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
kraken2	2.1.3	kraken2/2.1	None	application	Bioinformatics	Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
krakentools/py310	2.1	krakentools/py310/2.1	None	application	Bioinformatics	KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results.
krona	2.7.1	krona/2.7	None	application	bioinformatics	Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
kronos	2.3.0	kronos/2.3	None	application	workflow	Kronos is a highly flexible Python-based software tool that mainly enables bioinformatics developers, i.e. bioinformaticians who develop workflows for analyzing genomic data, to quickly make a workflow.
ksnp	3.1	ksnp/3.1	None	application	computational biology	kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.
lammps	07Aug2019	lammps/07Aug2019	compiler/gcc/11:openmpi/4.1	library	runtime support
lammps	23Jan2025	lammps/23Jan2025ml	compiler/nvhpc/24.5:openmpi/4.1	library	runtime support
lammps	23Jun2022	lammps/23June2022	compiler/gcc/11:openmpi/4.1	library	runtime support
lammps	27June2024	lammps/27June2024	compiler/gcc/11:openmpi/4.1 compiler/intel/20:openmpi/4.1	library	runtime support
lammps	29Sep2021	lammps/29Sep2021	compiler/gcc/10:openmpi/4.1 compiler/gcc/10:openmpi/4.0 compiler/gcc/11:openmpi/4.1 compiler/intel/19:openmpi/4.0 compiler/intel/20:openmpi/4.1	library	runtime support
lammps	2Aug2023	lammps/2Aug2023	compiler/intel/20:openmpi/4.1 compiler/gcc/11:openmpi/4.1	library	runtime support
lapack	3.9.1	lapack/3.9	compiler/gcc/9 compiler/intel/18 compiler/intel/20 compiler/pgi/20 compiler/gcc/10 compiler/intel/19 compiler/gcc/11	application	Utility	LAPACK is written in Fortran 90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.
lasagne	0.1	lasagne/py27/0.1	None	application	neural networks	A lightweight library to build and train neural networks in Theano
lasagne	0.1	lasagne/py36/0.1	None	application	neural networks	A lightweight library to build and train neural networks in Theano
lastools	v2.0.2	lastools/2.0	None	application	Geoscience	LASlib and LASzip libraries plus open source utilities from LAStools for manipulating LiDAR data in LAS format
lastz	1.04.22	lastz/1.04	None	application	computational biology	LASTZ is a program for aligning DNA sequences, a pairwise aligner.
lcms2	2.13.1	lcms2/2.13	compiler/intel/19 compiler/pgi/20 compiler/gcc/10 compiler/intel/20 compiler/gcc/9	library	runtime support
lefse	1.0.8.post1	lefse/1.0	None	application	computational biology	LEfSe (Linear discriminant analysis Effect Size) determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.
lefse	1.1.2	lefse/1.1	None	application	computational biology	LEfSe (Linear discriminant analysis Effect Size) determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.
lftp	4.8.3	lftp/4.8	None	application	system	LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).
lftp	4.9.1	lftp/4.9	None	application	system	LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).
libbeef	0.1.3	libbeef/0.1	compiler/intel/2024 compiler/intel/20 compiler/gcc/9 compiler/gcc/10 compiler/intel/19 compiler/pgi/20	application	Physics
libgeotiff	1.6.0	libgeotiff/1.6	compiler/intel/19 compiler/pgi/20 compiler/gcc/9 compiler/gcc/10 compiler/intel/20	library	runtime support
libidn	1.36	libidn/1.36	compiler/intel/19	library	runtime support
libint	2.6.0	libint/2.6	compiler/intel/20	library	runtime support
libjpeg	2.0.5	libjpeg/2.0	compiler/pgi/20 compiler/gcc/10 compiler/gcc/9 compiler/gcc/11 compiler/intel/20 compiler/intel/19	library	runtime support
libmesh	1.6.2	libmesh/1.6	compiler/gcc/10:openmpi/4.0	library	runtime support
libpng	1.6.37	libpng/1.6	compiler/gcc/11 compiler/gcc/9 compiler/gcc/10 compiler/pgi/20 compiler/intel/19 compiler/intel/20	library	runtime support
libtiff	4.1.0	libtiff/4.1	compiler/gcc/10 compiler/gcc/9 compiler/intel/20 compiler/gcc/11 compiler/intel/19 compiler/pgi/20	library	runtime support
libwebp	1.1.0	libwebp/1.1	compiler/intel/19 compiler/intel/20 compiler/gcc/10 compiler/pgi/20 compiler/gcc/9 compiler/gcc/11	library	runtime support
libxc	5.1.6	libxc/5.1	compiler/intel/19 compiler/gcc/10 compiler/intel/20 compiler/intel/2024 compiler/pgi/20 compiler/gcc/9	library	runtime support
libxc	5.2.0	libxc/5.2	compiler/intel/20 compiler/intel/2024 compiler/gcc/10 compiler/gcc/9 compiler/intel/19 compiler/pgi/20	library	runtime support
libxml2	2.9.9	libxml2/2.9	compiler/intel/20 compiler/intel/18 compiler/pgi/20 compiler/gcc/9 compiler/gcc/10 compiler/intel/19	library	runtime support
libxsmm	1.17	libxsmm/1.17	compiler/intel/20	library	runtime support
lmdb	0.9	lmdb/0.9	None	library	unknown	Lightning memory-mapped database library.
lmod	None	lmod	None	unknown	unknown	Lmod: An Environment Module System
lmod	lmod	lmod/lmod	None	unknown	unknown	Lmod: An Environment Module System
lofreq	2.1.3.1	lofreq/2.1	None	application	computational biology	LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data.
logomaker	0.8	logomaker/py27/0.8	None	application	Utility	Package for making Sequence Logos
logomaker	0.8	logomaker/py36/0.8	None	application	Utility	Package for making Sequence Logos
ls-bsr	0.0.2022.11.15	ls-bsr/2022.11.15	None	application	bioinformatics	Large scale Blast Score Ratio (BSR) analysis.
lsdyna	12.0.0	lsdyna/12	None	unknown	unknown
lsdyna	13.1.1	lsdyna/13.1	None	unknown	unknown
lsdyna	14.0.0	lsdyna/14.0	None	unknown	unknown
lumpy	0.0.2022.03.15	lumpy/2022.03.15	None	application	Tool
lynx	2.8.8	lynx/2.8	None	application	tool	Lynx is a text browser for the World Wide Web.
lyve-set	2.0.1	lyve-set/2.0	None	application	computational biology	LYVE version of the Snp Extraction Tool (SET), a method of using hqSNPs to create a phylogeny.
m4	1.0	m4/1.4	None	application	Utilities	The autotools collection is a set of tools that make it easy to build and install programs from a source distribution.
maaslin	0.0.5	maaslin/0.05	None	application	computational biology	MaAsLin is a multivariate statistical framework that finds associations between clinical metadata and microbial community abundance or function.
maaslin2	0.3.0	maaslin2/0.3	None	application	computational biology	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.
maaslin2	0.99.12	maaslin2/0.99	None	application	computational biology	MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.
macs2	2.1.1	macs2/2.1	None	application	computational biology	MACS -- Model-based Analysis of ChIP-Seq
macs2	2.2.9	macs2/2.2	None	application	computational biology	MACS -- Model-based Analysis of ChIP-Seq
macs3	3.0.2	macs3/3.0	None	application	computational biology	MACS -- Model-based Analysis of ChIP-Seq
maestro	1.5.1	maestro/1.5	None	application	computational biology	MAESTRO(Model-based AnalysEs of Single-cell Transcriptome and RegulOme) is a comprehensive single-cell RNA-seq and ATAC-seq analysis suit built using snakemake.
mafft	7.149	mafft/7.149	None	application	Bioinformatics	Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
mafft	7.407	mafft/7.407	None	application	Bioinformatics	Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
mafft	7.520	mafft/7.520	None	application	Bioinformatics	Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
mafft	7.526	mafft/7.526	None	application	Bioinformatics	Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
magicblast	1.7.0	magicblast/1.7	None	application	computational biology	NCBI BLAST next generation read mapper
make	1.0	make/4.3	None	application	Utilities	The autotools collection is a set of tools that make it easy to build and install programs from a source distribution.
maker	2.31.10	maker/2.31	None	application	computational biology	MAKER is a genome annotation pipeline for prokaryotic and smaller eukaryotic organisms.
maker	3.01.03	maker/3.01	None	application	computational biology	MAKER is a genome annotation pipeline for prokaryotic and smaller eukaryotic organisms.
mamba	0.13.0	mamba/0.13	None	application	system
mamba	0.15.3	mamba/0.15	None	application	system
mamba	0.5.1	mamba/0.5.1	None	application	system
mamba	0.7.3	mamba/0.7	None	application	system
mamba	23.1.0/1.3.1	mamba/1.3	None	application	system
mamba	23.11.0/1.5.4	mamba/1.5	None	application	system
mamba	23.7.2/1.4.9	mamba/1.4	None	application	system
mamba	4.12.0/0.24.0	mamba/0.24	None	application	system
manorm	1.3.0	manorm/py36/1.3	None	application	genomics	A robust model for quantitative comparison of ChIP-Seq data sets.
manorm	1.3.0	manorm/py38/1.3	None	application	genomics	A robust model for quantitative comparison of ChIP-Seq data sets.
manta	1.6.0	manta/1.6	None	application	Structural variant	Structural variant and indel caller for mapped sequencing data
mapping-iterative-assembler	1.0	mapping-iterative-assembler/1.0	None	application	bioinformatics	Consensus calling or `reference assisted assembly`, chiefly of ancient mitochondria.
mapsplice	2.2.0	mapsplice/2.2	None	application	computational biology	MapSplice is a software for mapping RNA-seq data to reference genome for splice junction discovery that depends only on reference genome, and not on any further annotations.
maq	0.7	maq/0.7	None	application	computational biology	maq - Mapping and Assembly with Quality.
mash	2.2.2	mash/2.2	None	application	computational biology	Fast sequence distance estimator that uses MinHash
mashmap	2.0	mashmap/2.0	None	application	computational biology	A fast approximate aligner for long DNA sequences
mashmap	3.1.1	mashmap/3.1	None	application	computational biology	A fast approximate aligner for long DNA sequences
mashtree	1.4.6	mashtree/1.4	None	application	computational biology	Create a tree using Mash distances
masurca	3.3.1	masurca/3.3	None	application	Biology	MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software. MaSuRCA requires Illumina data, and supports third-generation PacBio/Nanopore MinION reads for hybrid assembly.
masurca	4.0.9	masurca/4.0	None	application	Biology	MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software. MaSuRCA requires Illumina data, and supports third-generation PacBio/Nanopore MinION reads for hybrid assembly.
masurca	4.1.0	masurca/4.1	None	application	Biology	MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software. MaSuRCA requires Illumina data, and supports third-generation PacBio/Nanopore MinION reads for hybrid assembly.
mathematica	11.0	mathematica/11.0	None	application	Engineering
mathematica	11.3	mathematica/11.3	None	application	Engineering
mathematica	12.0	mathematica/12.0	None	application	Engineering
mathematica	12.3	mathematica/12.3	None	application	Engineering
mathematica	13.1	mathematica/13.1	None	application	Engineering
mathematica	13.2	mathematica/13.2	None	application	Engineering
mathematica	14.2	mathematica/14.2	None	application	Engineering
matio	1.5	matio/1.5	compiler/gcc/10	library	runtime support
matlab	r2012b	matlab/r2012b	None	unknown	unknown
matlab	r2013b	matlab/r2013b	None	unknown	unknown
matlab	r2014b	matlab/r2014b	None	unknown	unknown
matlab	r2015b	matlab/r2015b	None	unknown	unknown
matlab	r2016a	matlab/r2016a	None	unknown	unknown
matlab	r2016b	matlab/r2016b	None	unknown	unknown
matlab	r2017a	matlab/r2017a	None	unknown	unknown
matlab	r2017b	matlab/r2017b	None	unknown	unknown
matlab	r2018a	matlab/r2018a	None	unknown	unknown
matlab	r2018b	matlab/r2018b	None	unknown	unknown
matlab	r2019a	matlab/r2019a	None	unknown	unknown
matlab	r2019b	matlab/r2019b	None	unknown	unknown
matlab	r2020a	matlab/r2020a	None	unknown	unknown
matlab	r2020b	matlab/r2020b	None	unknown	unknown
matlab	r2021a	matlab/r2021a	None	unknown	unknown
matlab	r2021b	matlab/r2021b	None	unknown	unknown
matlab	r2022a	matlab/r2022a	None	unknown	unknown
matlab	r2022b	matlab/r2022b	None	unknown	unknown
matlab	r2023a	matlab/r2023a	None	unknown	unknown
matlab	r2023b	matlab/r2023b	None	unknown	unknown
matlab	r2024a	matlab/r2024a	None	unknown	unknown
mauve	2.4	mauve/2.4	None	application	computational biology	mauve - Multiple Genome Alignment.
maven	3.2	maven/3.2	None	application	system	Apache Maven is a software project management and comprehension tool.
maven	3.5	maven/3.5	None	application	system	Apache Maven is a software project management and comprehension tool.
maxbin2	2.2.7	maxbin2/2.2	None	application	Biology	MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.
maxquant	1.6.10.43	maxquant/1.6	None	application	biochemistry	MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted.
maxquant	2.0.3.0	maxquant/2.0	None	application	biochemistry	MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted.
mbuffer	20171011	mbuffer/20171011	None	application	buffer	Mbuffer is a tool for buffering data streams with a large set of unique features.
mcl	14.137	mcl/14.137	None	application	computational biology	MCL
medaka	1.7.2	medaka/py38/1.7	None	application	bioinformatics	Neural network sequence error correction.
medaka-gpu	1.7.2	medaka-gpu/py38/1.7	None	application	bioinformatics	Neural network sequence error correction.
meep	1.3	meep/1.3	None	library	runtime support
meerkat	0.189	meerkat/0.1	None	application	computational biology	Meerkat is designed to identify structural variations
megahit	1.1	megahit/1.1	None	application	computational biology	MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
megahit	1.2.9	megahit/1.2	None	application	computational biology	MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
megahit-gpu	1.1	megahit-gpu/1.1	None	application	computational biology	MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
megalodon	2.4.1	megalodon/2.4	None	application	Genomics	Nanopore modified base and sequence variant detection.
megalodon	2.5.0	megalodon/2.5	None	application	Genomics	Nanopore modified base and sequence variant detection.
megalodon-gpu	2.5.0	megalodon-gpu/2.5	None	application	Bioinformatics	Nanopore modified base and sequence variant detection.
megan	6.12.3	megan/6.12	None	application	Computational Biology	A tool for studying the taxonomic content of a set of DNA reads
megan	6.25.9	megan/6.25	None	application	Computational Biology	A tool for studying the taxonomic content of a set of DNA reads
melonnpan	2019.03.22	melonnpan/2019.03.22	None	application	computational biology	MelonnPan is a computational method for predicting metabolite compositions from shotgun metagenomic sequencing data.
merqury	1.3	merqury/1.3	None	application	Genome Analysis	Evaluate genome assemblies with k-mers and more.
meryl	1.4.1	meryl/1.4	None	application	genome analysis	A genomic k-mer counter (and sequence utility) with nice features
meson	0.61.1	meson/0.61	None	application	Utilities	The Meson Build System
meson	1.8.0	meson/1.8	None	application	Utilities	The Meson Build System
metabat2	2.15	metabat2/2.15	None	application	computational biology	Metagenome binning
metabolic	20210303	metabolic/20210303	None	application	Bioinformatics	A scalable high-throughput metabolic and biogeochemical functional trait profiler.
metacv	2.3.0	metacv/2.3	None	application	Bioinformatics	Composition based classification for short metagenomic sequences
metaphlan	1.7	metaphlan/1.7	None	application	metagenomic phylogenetic analysis	MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metaphlan	3.0.3	metaphlan/3.0	None	application	metagenomic phylogenetic analysis	MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metaphlan	3.1.0	metaphlan/3.1	None	application	metagenomic phylogenetic analysis	MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metaphlan	4.0.6	metaphlan/4.0	None	application	metagenomic phylogenetic analysis	MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metaphlan	4.1.1	metaphlan/4.1	None	application	metagenomic phylogenetic analysis	MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metaphlan2	2.6.0	metaphlan2/2.6	None	application	metagenomic phylogenetic analysis	MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metaphlan2	2.7.8	metaphlan2/2.7	None	application	metagenomic phylogenetic analysis	MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metaphlan2	2.96.1	metaphlan2/2.96	None	application	metagenomic phylogenetic analysis	MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metasnv	2.0.1	metasnv/2.0	None	application	Biology	SNV calling software
metasv	0.5.4	metasv/0.5	None	application	computational biology	An accurate and integrative structural-variant caller for next generation sequencing.
metavelvet	1.2.01	metavelvet/1.2	None	application	computational biology	MetaVelvet is an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.
metawrap	1.1	metawrap/1.1	None	application	computational biology	MetaWRAP is a pipeline for genome-resolved metagenomic data analysis
metawrap	1.2	metawrap/1.2	None	application	computational biology	MetaWRAP is a pipeline for genome-resolved metagenomic data analysis
metawrap	1.3.2	metawrap/1.3	None	application	computational biology	MetaWRAP is a pipeline for genome-resolved metagenomic data analysis
metaxa2	2.2.3	metaxa2/2.2	None	application	classification	Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data.
methylpy	1.4.1	methylpy/py27/1.4	None	application	bioinformatics	Bisulfite sequencing data processing and differential methylation analysis
methylpy	1.4.1	methylpy/py36/1.4	None	application	bioinformatics	Bisulfite sequencing data processing and differential methylation analysis
methylpy	1.4.1	methylpy/py37/1.4	None	application	bioinformatics	Bisulfite sequencing data processing and differential methylation analysis
metis	4.0.0	metis/4.0	compiler/gcc/9	library	runtime support
metis	5.1.0	metis/5.1	compiler/pgi/20 compiler/intel/19 compiler/gcc/9 compiler/intel/20 compiler/gcc/10	library	runtime support
mfold	3.6	mfold/3.6	None	application	computational biology	Mfold web server for nucleic acid folding and hybridization prediction.
mgblast	2.2.14	mgblast/2.2	None	application	Alignment	fast all-vs-all DNA alignment tool, modification of megablast from a 2006 version of NCBI C Toolkit
mgltools	1.5.7	mgltools/1.5	None	application	computational structural biology	MGLTools is an program for visualization and analisys of molecular structures.
miRDeep	2.0.0	miRDeep/2.0	None	application	computational biology	miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.
micropita	1.1.0	micropita/1.1	None	application	computational biology	microPITA is a computational tool enabling sample selection in two-stage (tiered) studies.
midas	1.3.2	midas/1.3	None	application	computational biology	An integrated pipeline for estimating strain-level genomic variation from metagenomic data
midnight-commander	4.8.22	midnight-commander/4.8	None	application	Utility	GNU Midnight Commander is a visual file manager, licensed under GNU General Public License and therefore qualifies as Free Software. It's a feature rich full-screen text mode application that allows you to copy, move and delete files and whole directory trees, search for files and run commands in the subshell. Internal viewer and editor are included.
minibusco	0.2.1	minibusco/0.2	None	application	bioinformatics	minibusco: a faster and more accurate reimplementation of BUSCO
miniforge	24.5.0/1.5.8	miniforge/24.5	None	application	system
minimap2	2.16	minimap2/2.16	None	application	bioinformatics	A versatile pairwise aligner for genomic and spliced nucleotide sequences.
minimap2	2.26	minimap2/2.26	None	application	bioinformatics	A versatile pairwise aligner for genomic and spliced nucleotide sequences.
minpack	19961126	minpack/19961126	compiler/pgi/20 compiler/intel/20 compiler/gcc/10 compiler/intel/19 compiler/gcc/9	application	Utility	Minpack includes software for solving nonlinear equations and nonlinear least squares problems.
miranda	3.3a	miranda/3.3a	None	application	computational biology	An algorithm for finding genomic targets for microRNAs
misis	1.0	misis/1.0	None	application	computational biology
mitosalt	1.1.1	mitosalt/1.1	None	application	computational biology	Identification of mitochondrial structural alterations.
mitoz	3.6	mitoz/3.6	None	application	computational biology	MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
mldata	1.0	mldata/1.0	None	application	computer science	Static data resources for machine-learning/AI.
mlflow	2.16.2	mlflow/py310/2.16	None	application	machine learning	MLflow is an open source platform for the machine learning lifecycle.
mlflow	2.16.2	mlflow/py312/2.16	None	application	machine learning	MLflow is an open source platform for the machine learning lifecycle.
mlpack	2.2.5	mlpack/2.2	None	application	Machine Learning	mlpack a fast, flexible machine learning library
mlpack	3.0.3	mlpack/3.0	None	application	Machine Learning	mlpack a fast, flexible machine learning library
mlst	2.16.2	mlst/2.16	None	application	computational biology	Scan contig files against PubMLST typing schemes
mlst	2.19.0	mlst/2.19	None	application	computational biology	Scan contig files against PubMLST typing schemes
mlst	2.22.0	mlst/2.22	None	application	computational biology	Scan contig files against PubMLST typing schemes
mmseqs2	13.45111	mmseqs2/13.45111	compiler/gcc/9:openmpi/4.0 compiler/gcc/11:openmpi/4.1 compiler/gcc/10:openmpi/4.0	application	Bioinformatics	MMseqs2: ultra fast and sensitive search and clustering suite.
modeller	9.19	modeller/9.19	None	unknown	unknown
modflow-2005	1.12.00	modflow-2005/1.12	None	application	USGS	Three-dimensional finite-difference ground-water flow model.
modflow6	6.6.1	modflow6/6.6	None	application	USGS	USGS Modular Hydrologic Model
moleman2	2021.10.26	moleman2/20211026	compiler/gcc/10	application	crystallographic map
mongodb-client	3.2	mongodb-client/3.2	None	application	Utility	Client programs for MongoDB.
mongodb-client	3.4	mongodb-client/3.4	None	application	Utility	Client programs for MongoDB.
mongodb-client	4.2	mongodb-client/4.2	None	application	Utility	Client programs for MongoDB.
mono	4.6	mono/4.6	None	application	compiler	Mono is a software platform designed to allow developers to easily create cross platform applications.
mono	5.10	mono/5.10	None	application	compiler	Mono is a software platform designed to allow developers to easily create cross platform applications.
mono	5.14.0.177	mono/5.14	None	application	compiler	Mono is a software platform designed to allow developers to easily create cross platform applications.
morgan	3.4	morgan/3.4	None	application	computational biology	MORGAN is part of our software for Markov chain Monte Carlo in Genetic Analysis.
mosaik	2.2	mosaik/2.2	None	application	computational biology	MOSAIK is a reference-guided aligner for next-generation sequencing technologies.
mosdepth	0.2.4	mosdepth/0.2	None	application	computational biology	Fast BAM/CRAM depth calculation for WGS, exome, or targetted sequencing.
mosdepth	0.3.8	mosdepth/0.3	None	application	computational biology	Fast BAM/CRAM depth calculation for WGS, exome, or targetted sequencing.
mothur	1.41.3	mothur/1.41	None	application	Bioinformatics	This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
mothur	1.45.3	mothur/1.45	None	application	Bioinformatics	This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
mothur	1.46.1	mothur/1.46	None	application	Bioinformatics	This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
mpfr	4.1.0	mpfr/4.1	compiler/gcc/10	library	runtime support	The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
mpich	3.4	mpich/3.4	compiler/gcc/9	library	runtime support
mpich	4.0	mpich/4.0	compiler/gcc/10	library	runtime support
mpich2	1.5	mpich2/1.5	compiler/gcc/9	library	runtime support
mplus	6.12	mplus/6.12	None	application	unknown	Mplus is a latent variable modeling program with a wide variety of analysis capabilities.
mplus	7.0	mplus/7.0	None	application	unknown	Mplus is a latent variable modeling program with a wide variety of analysis capabilities.
mrbayes	3.2.7	mrbayes/3.2	None	application	computational biology	Bayesian Inference of Phylogeny
mridata	1.0	mridata/1.0	None	application	brain imaging	Static data resources for MRI/NeuroImaging.
mrtrix3	3.0.4	mrtrix3/3.0	None	application	computational neuroimaging	Advanced tools for the analysis of diffusion MRI data.
mrtrix3tissue	5.2.9	mrtrix3tissue/5.2	None	application	computational neuroimaging	MRtrix3Tissue adds capabilities for 3-Tissue CSD modelling and analysis to a complete version of MRtrix3.
msgf_plus	2020.06.22	msgf_plus/2020.06.22	None	application	proteomics	MS-GF+ is a new MS/MS database search tool that is sensitive (it identifies more peptides than other database search tools and as many peptides as spectral library search tools) and universal (works well for diverse types of spectra, different configurations of MS instruments and different experimental protocols).
msms	2.6.1	msms/2.6	None	application	computational biology	MSMS is a program written in the C programming language to compute molecular surfaces.
mspkmercounter	0.10.0	mspkmercounter/0.10	None	application	Biology	MSPKmerCounter is a k-mer counter based on the minimum substring partitioning technique.
mugsy	1.2.3	mugsy/1.2	None	application	computational biology	Mugsy is a multiple whole genome aligner.
mujoco	2.1.0	mujoco/2.1	None	application	Simulation	MuJoCo | advanced physics simulation.
mujoco	200	mujoco/200	None	application	Simulation	MuJoCo | advanced physics simulation.
multigps	0.74	multigps/0.74	None	application	computational biology	MultiGPS is a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing differential binding events between conditions.
multiqc	0.8	multiqc/py27/0.8	None	application	computational biology	MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiqc	0.8	multiqc/py35/0.8	None	application	computational biology	MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiqc	1.6	multiqc/py27/1.6	None	application	computational biology	MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiqc	1.6	multiqc/py35/1.6	None	application	computational biology	MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiqc	1.6	multiqc/py36/1.6	None	application	computational biology	MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiqc	1.8	multiqc/py27/1.8	None	application	computational biology	MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiqc	1.8	multiqc/py37/1.8	None	application	computational biology	MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiwfn	3.8	multiwfn/3.8	compiler/intel/18	application	Wavefunction	Multiwfn is a powerful program for realizing electronic wavefunction analysis, which is a key ingredient of quantum chemistry.
mumax3	3.10	mumax3/3.10	None	application	micromagnetics	GPU-accelerated micromagnetic simulator
mumax3	3.9.3	mumax3/3.9	None	application	micromagnetics	GPU-accelerated micromagnetic simulator
mumaxplus	1.0.0	mumaxplus/py39/1.0	None	application	micromagnetics	More versatile and extensible GPU-accelerated micromagnetic simulator.
mumaxplus	1.0.0	mumaxplus/py310/1.0	None	application	micromagnetics	More versatile and extensible GPU-accelerated micromagnetic simulator.
mummer	3.23	mummer/3.23	None	application	bioinformatics	MUMmer is a system for rapidly aligning entire genomes
mummer4	4.0.0beta2	mummer4/4.0	None	application	Bioinformatics	MUMmer is a system for rapidly aligning entire genomes
muscle	3.8.1551	muscle/3.8	None	application	computational biology	MUSCLE: multiple sequence alignment with high accuracy and high throughput
muscle	5.1	muscle/5.1	None	application	computational biology	MUSCLE: multiple sequence alignment with high accuracy and high throughput
music	1.0	music/1.0	None	application	computational biology	MUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.
mutect	1.1	mutect/1.1	None	application	computational biology	MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.
mxnet	0.9.3a	mxnet/0.9.3	None	application	AI	MXNet is an open-source deep learning framework that allows you to define, train, and deploy deep neural networks on a wide array of devices, from cloud infrastructure to mobile devices.
mxnet	1.5.0	mxnet/1.5	None	application	AI	MXNet is an open-source deep learning framework that allows you to define, train, and deploy deep neural networks on a wide array of devices, from cloud infrastructure to mobile devices.
mysql-client	8.0.23	mysql-client/8.0	None	application	Database	MySQL client applications and tools
mytaxa	1.0	mytaxa/1.0	None	application	computational biology	MyTaxa - Assign taxonomy to metagenomic fragments.
namd	3.0.1	namd/3.0	compiler/gcc/11:openmpi/4.1	application	molecular dynamics	NAMD, recipient of a 2002 Gordon Bell Award, a 2012 Sidney Fernbach Award, and a 2020 Gordon Bell Prize, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
namd-gpu	3.0.1	namd-gpu/3.0	None	application	molecular dynamics	NAMD, recipient of a 2002 Gordon Bell Award, a 2012 Sidney Fernbach Award, and a 2020 Gordon Bell Prize, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
nano	2.9.8	nano/2.9	None	application	Utility	Nano's ANOther editor, an enhanced free Pico clone
nano	5.5	nano/5.5	None	application	Utility	Nano's ANOther editor, an enhanced free Pico clone
nano	5.7	nano/5.7	None	application	Utility	Nano's ANOther editor, an enhanced free Pico clone
nano	6.2	nano/6.2	None	application	Utility	Nano's ANOther editor, an enhanced free Pico clone
nano	8.2	nano/8.2	None	application	Utility	Nano's ANOther editor, an enhanced free Pico clone
nanofilt	2.8.0	nanofilt/2.8	None	application	Bioinformatics	Filtering and trimming of Oxford Nanopore Sequencing data
nanoplot	1.40.2	nanoplot/1.40	None	application	computational biology	Plotting suite for long read sequencing data and alignments
nanopolish	0.14.0	nanopolish/0.14	None	application	bioinformatics	Signal-level algorithms for MinION data.
ncbi-amrfinderplus	3.8.4	ncbi-amrfinderplus/3.8	None	application	bioinformatics	AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
ncbi-datasets-cli	16.4.4	ncbi-datasets-cli/16.4	None	application	bioinformatics	NCBI Datasets command-line clients
ncbi-download	0.2.6	ncbi-download/0.2	None	application	computational biology	Python scriopt for downloading bacterial and fungal genomes from NCBI.
ncbi-download	0.3.3	ncbi-download/0.3	None	application	computational biology	Python scriopt for downloading bacterial and fungal genomes from NCBI.
ncdu	1.15	ncdu/1.15	None	application	System	NCurses Disk Usage
ncl	6.6.2	ncl/6.6	None	application	utility	NCAR Command Language
nco	4.8.1	nco/4.8	None	library	runtime support	Suite of programs for manipulating NetCDF/HDF4 files.
ncview	2.1.7	ncview/2.1	compiler/intel/20 compiler/pgi/20	library	runtime support	Ncview is a visual browser for netCDF format files.
nda-tools	0.2.23	nda-tools/0.2	None	application	NDA web services	Python package for interacting with NDA web services.
neper	3.3.0	neper/3.3	None	application	Applications	Neper is a software package for polycrystal generation and meshing.
neper	3.5.2	neper/3.5	None	application	Applications	Neper is a software package for polycrystal generation and meshing.
neptune	1.2.5	neptune/1.2	None	application	computational biology	Neptune locates genomic signatures using an exact k-mer matching strategy while accommodating k-mer mismatches.
netcdf	4.2	netcdf/4.2	compiler/intel/18	library	runtime support
netcdf	4.4	netcdf/4.4	compiler/gcc/9	library	runtime support
netcdf	4.4.0	netcdf/4.4	compiler/intel/18	library	runtime support
netcdf	4.5.0	netcdf/4.5	compiler/gcc/10 compiler/intel/19 compiler/gcc/9 compiler/intel/20	library	runtime support
netcdf	4.7	netcdf/4.7	compiler/pgi/20	library	runtime support
netcdf	4.7.0	netcdf/4.7	compiler/intel/19 compiler/intel/20	library	runtime support
netcdf	4.7.4	netcdf/4.7	compiler/gcc/9 compiler/gcc/10 compiler/gcc/11	library	runtime support
netica-c	5.04	netica-c/5.04	compiler/gcc/9	library	mathematics
netlogo	6.2.2	netlogo/6.2	None	application	Simulation	NetLogo is a multi-agent programmable modeling environment
netsurfp	1.0c	netsurfp/1.0	None	application	computational biology	NetSurfP predicts the surface accessibility and secondary structure of amino acids in an amino acid sequence. The method also simultaneously predicts the reliability for each prediction, in the form of a Z-score. The Z-score is related to the surface prediction, and not the secondary structure.
nextdenovo	2.5.0	nextdenovo/2.5	None	application	Bioinformatics	String graph-based de novo assembler for long reads (CLR, HiFi and ONT)
nextflow	20.04.1	nextflow/20.04	None	application	computational pipeline	A DSL for data-driven computational pipelines http://nextflow.io
nextflow	21.04.0	nextflow/21.04	None	application	computational pipeline	A DSL for data-driven computational pipelines http://nextflow.io
nextflow	21.10.6	nextflow/21.10	None	application	computational pipeline	A DSL for data-driven computational pipelines http://nextflow.io
nextflow	22.10.6	nextflow/22.10	None	application	computational pipeline	A DSL for data-driven computational pipelines http://nextflow.io
nextflow	23.04.1	nextflow/23.04	None	application	computational pipeline	A DSL for data-driven computational pipelines http://nextflow.io
nextflow	23.10.1	nextflow/23.10	None	application	computational pipeline	A DSL for data-driven computational pipelines http://nextflow.io
nextflow	24.04.3	nextflow/24.04	None	application	computational pipeline	A DSL for data-driven computational pipelines http://nextflow.io
nextpolish	1.4.1	nextpolish/1.4	None	application	computational biology	Fast and accurately polish the genome generated by long reads
nextstrain-cli	1.16.2	nextstrain-cli/1.16	None	application	computational biology	Nextstrain: analysis and visualization of pathogen sequence data.
nextstrain-cli	3.0.3	nextstrain-cli/3.0	None	application	computational biology	Nextstrain: analysis and visualization of pathogen sequence data.
nextstrain-cli	3.2.5	nextstrain-cli/3.2	None	application	computational biology	Nextstrain: analysis and visualization of pathogen sequence data.
nextstrain-cli	4.2.0	nextstrain-cli/4.2	None	application	computational biology	Nextstrain: analysis and visualization of pathogen sequence data.
ngmlr	0.2.7	ngmlr/0.2	None	application	computational biology	ngmlr is a long-read mapper designed to align PacBio or Oxford Nanopore reads to a reference genome and optimized for structural variation detection
ninja	1.10.2	ninja/1.10	None	application	Utility	A small build system with a focus on speed
ninja	1.12.1	ninja/1.12	None	application	Utility	A small build system with a focus on speed
nlopt	2.7.1	nlopt/py39/2.7	None	application	algorithms	nonlinear optimization library
nodejs	16.6.1	nodejs/16.6	None	application	system	a platform for easily building fast, scalable network applications
nofold	1.0.1	nofold/1.0	None	application	computational biology	NoFold is an approach for characterizing and clustering RNA secondary structures without computational folding or alignment.
nomad	2.0.0	nomad/2.0	None	application	computational biology	NOMAD is an unsupervised and reference-free unifying framework to discover regulated sequence variation through statistical analysis of k-mer composition in both DNA and RNA sequence.
nquire	2018.04.05	nquire/2018.04.05	None	application	computational biology	A statistical framework for ploidy estimation using NGS short-read data.
nucdiff	2.0.2	nucdiff/2.0	None	application	computational biology	NucDiff locates and categorizes differences between two closely related nucleotide sequences.
nvim	0.9.5	nvim/0.9	None	application	utility	Ambitious Vim-fork focused on extensibility and agility
nwchem	7.0.2	nwchem/7.0	compiler/gcc/9:openmpi/4.1	library	runtime support
nwchem	7.2.2	nwchem/7.2	compiler/gcc/9:openmpi/4.1	library	runtime support
oases	0.2.09	oases/0.2	None	application	computational biology	Oases is de novo transcriptome assembler based on the Velvet genome assembler core.
octave	4.2	octave/4.2	None	application	engineering	GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.
octave	6.1	octave/6.1	None	application	engineering	GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.
octave	6.2	octave/6.2	None	application	engineering	GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.
octave	7.2	octave/7.2	None	application	engineering	GNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.
octopus	13.0	octopus/13.0	compiler/intel/20:openmpi/4.1	application	Applications
oma	2.4.1	oma/2.4	None	application	genomics	OMA standalone is a standalone package that can infer orthologs using the OMA algorithm on custom genomes.
oncodriveclustl	1.1.3	oncodriveclustl/1.1	None	application	Biology	OncodriveCLUSTL is a clustering method to identify cancer drivers
oncotator	1.9.9.0	oncotator/1.9	None	application	computational biology	Oncotator is a tool for annotating human genomic point mutations and indels with data relevant to cancer researchers.
openbabel	3.1.1	openbabel/py37/3.1	None	application	chemistry	A chemical toolbox designed to speak the many languages of chemical data
openbabel	3.1.1	openbabel/py38/3.1	None	application	chemistry	A chemical toolbox designed to speak the many languages of chemical data
openblas	0.3.18	openblas/0.3	compiler/gcc/10 compiler/gcc/9	library	tools	Numerical library, contains blas/lapack
openbugs	3.2	openbugs/3.2	None	application	statistics	BUGS is a software package for performing Bayesian inference Using Gibbs Sampling.
opencl	2025.0.4	opencl/2025.0	compiler/gcc/9	library	unknown	This runtime software package adds OpenCL CPU device support on systems with Intel Core and Intel Xeon processors.
opencv	2.4.11	opencv/2.4	None	library	unknown	Open Source Computer Vision Library
opencv	3.1.0	opencv/3.1	None	library	unknown	Open Source Computer Vision Library
opencv	3.4.1	opencv/py27/3.4	None	library	unknown	Open Source Computer Vision Library
opencv	3.4.1	opencv/py36/3.4	None	library	unknown	Open Source Computer Vision Library
opencv	4.2.0	opencv/py27/4.2	None	library	unknown	Open Source Computer Vision Library
opencv	4.2.0	opencv/py37/4.2	None	library	unknown	Open Source Computer Vision Library
opencv	4.2.0	opencv/py38/4.2	None	library	unknown	Open Source Computer Vision Library
opencv	4.5.5	opencv/4.5	compiler/gcc/11	library	unknown	Open Source Computer Vision Library
opencv	4.8.1	opencv/4.8	compiler/gcc/11	library	unknown	Open Source Computer Vision Library
openfoam	9	openfoam/9.0	compiler/gcc/11:openmpi/4.1	library	runtime support
openjdk	10	openjdk/10	None	application	system	OpenJDK (Java).
openjdk	11	openjdk/11	None	application	system	OpenJDK (Java).
openjdk	12	openjdk/12	None	application	system	OpenJDK (Java).
openjdk	13	openjdk/13	None	application	system	OpenJDK (Java).
openjdk	14	openjdk/14	None	application	system	OpenJDK (Java).
openjdk	15	openjdk/15	None	application	system	OpenJDK (Java).
openjdk	16	openjdk/16	None	application	system	OpenJDK (Java).
openjdk	17	openjdk/17	None	application	system	OpenJDK (Java).
openjdk	18	openjdk/18	None	application	system	OpenJDK (Java).
openjdk	19	openjdk/9	None	application	system	OpenJDK (Java).
openjdk	19	openjdk/19	None	application	system	OpenJDK (Java).
openjdk	20	openjdk/20	None	application	system	OpenJDK (Java).
openjdk	21	openjdk/21	None	application	system	OpenJDK (Java).
openjdk	22	openjdk/22	None	application	system	OpenJDK (Java).
openjdk	23	openjdk/23	None	application	system	OpenJDK (Java).
openjpeg	2.3.1	openjpeg/2.3	compiler/pgi/20	library	runtime support
openjpeg	2.4	openjpeg/2.4	compiler/pgi/20 compiler/intel/20 compiler/intel/19 compiler/gcc/9 compiler/gcc/10	library	runtime support
openmolcas	23.06	openmolcas/23.06	compiler/intel/20:openmpi/4.1	application	quantum chemistry software package	OpenMolcas is a quantum chemistry software package developed by scientists and intended to be used by scientists. It includes programs to apply many different electronic structure methods to chemical systems, but its key feature is the multiconfigurational approach, with methods like CASSCF and CASPT2.
openmpi	3.1	openmpi/3.1	compiler/nvhpc/21.9	library	runtime support
openmpi	4.0	openmpi/4.0	compiler/intel/16 compiler/pgi/20 compiler/intel/20 compiler/intel/19 compiler/intel/18 compiler/gcc/11 compiler/gcc/9 compiler/gcc/10	library	runtime support
openmpi	4.1	openmpi/4.1	compiler/intel/20 compiler/gcc/10 compiler/intel/19 compiler/intel/2024 compiler/gcc/11 compiler/nvhpc/24.5 compiler/nvhpc/25.3 compiler/gcc/9 compiler/intel/2021 compiler/intel/18 compiler/pgi/20	library	runtime support
openmx	3.9	openmx/3.9	compiler/intel/20:openmpi/4.0 compiler/intel/20:openmpi/4.1	library	runtime support
openslide	3.4.1	openslide/3.4	None	application	images	OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides).
optuna	2.8.0	optuna/py37/2.8	None	application	Mathematics	A hyperparameter optimization framework
optuna	2.8.0	optuna/py38/2.8	None	application	Mathematics	A hyperparameter optimization framework
optuna	2.8.0	optuna/py39/2.8	None	application	Mathematics	A hyperparameter optimization framework
orca	5.0.4	orca/5.0	compiler/gcc/11:openmpi/4.1	application	quantum chemistry	ORCA is an ab initio, DFT, and semi-empirical SCF-MO package.
orca	6.0.0	orca/6.0	compiler/gcc/11:openmpi/4.1	application	quantum chemistry	ORCA is an ab initio, DFT, and semi-empirical SCF-MO package.
orthofinder	1.1.8	orthofinder/1.1	None	application	computational biology	OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics.
orthofinder	2.2.6	orthofinder/2.2	None	application	computational biology	OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics.
orthofinder	2.5.5	orthofinder/2.5	None	application	computational biology	OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics.
orthomcl	2.0.9	orthomcl/2.0	None	application	Biology	Ortholog groups of protein sequences
p7zip	16.02	p7zip/16.02	None	application	System	p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org ) for Unix.
paml	4.9	paml/4.9	None	application	Sequencing	Phylogenetic Analysis by Maximum Likelihood (PAML)
pandaseq	2.11	pandaseq/2.11	None	application	bioinformatics	PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
panphlan	1.3	panphlan/1.3	None	application	biology	PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and in-vivo transcriptional activity of individual strains in metagenomic samples.
panphlan	3.0	panphlan/3.0	None	application	biology	PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition and in-vivo transcriptional activity of individual strains in metagenomic samples.
parallel-fastq-dump	0.6.5	parallel-fastq-dump/0.6	None	application	bioinformatics	parallel fastq-dump wrapper
paraview	5.10.1	paraview/py37/5.10	None	application	Utility	ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview	5.10.1	paraview/py38/5.10	None	application	Utility	ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview	5.10.1	paraview/py39/5.10	None	application	Utility	ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview	5.11.1	paraview/py39/5.11	None	application	Utility	ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview	5.11.1	paraview/py310/5.11	None	application	Utility	ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview	5.11.1	paraview/py311/5.11	None	application	Utility	ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview	5.9.1	paraview/py37/5.9	None	application	Utility	ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview	5.9.1	paraview/py38/5.9	None	application	Utility	ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview	5.9.1	paraview/py39/5.9	None	application	Utility	ParaView is an open-source, multi-platform data analysis and visualization application based on Visualization Toolkit (VTK).
paraview-headless	5.10	paraview-headless/5.10	compiler/gcc/11:openmpi/4.1	application	Visualization
parmetis	4.0.3	parmetis/4.0	compiler/intel/20:openmpi/4.0 compiler/pgi/20:openmpi/4.0 compiler/gcc/9:openmpi/4.0 compiler/intel/19:openmpi/4.0 compiler/intel/20:openmpi/4.1 compiler/gcc/10:openmpi/4.0 compiler/gcc/11:openmpi/4.1	library	runtime support
parsinsert	1.04	parsinsert/1.04	None	application	computational biology	ParsInsert efficiently produces both a phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis. This is a C++ implementation of the Parsimonious Insertion algorithm
parsnp	2.1.3	parsnp/2.1	None	application	computational biology	Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection.
pasa	2.3.3	pasa/2.3	None	application	computational biology	PASA
pb-assembly	0.0.8	pb-assembly/0.0.8	None	application	Genomics	Meta-package for Falcon/Unzip tool-suite (originally by Jason Chin)
pbh5tools	0.8.0	pbh5tools/0.8	None	application	computational biology	pbh5tools -- tools for manipulating HDF5 files produced by Pacific Biosciences. Specifically, this package provides functionality for manipulating and extracting data from "cmp.h5" and "bas.h5" files.
pblat	2.0	pblat/2.0	None	application	computational biology
pbmm2	2.10.0	pbmm2/1.16	None	application	Bioinformatics	A minimap2 frontend for PacBio native data formats
pbsv	2.10.0	pbsv/2.10	None	application	Bioinformatics	PacBio structural variant (SV) calling and analysis tools
peakranger	1.18	peakranger/1.18	None	application	computational biology	PeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data.
peakzilla	1.0	peakzilla/1.0	None	application	computational biology	Peakzilla identifies sites of enrichment and transcription factor binding sites from transcription factor ChIP-seq and ChIP-exo experiments at hight accuracy and resolution.
pegasus-wms	5.0	pegasus-wms/5.0	None	application	workflow management system	Pegasus Workflow Management System
pepr	1.1.18	pepr/1.1	None	application	computational biology	Peak-calling and Prioritization pipeline for replicated ChIP-Seq data.
perl	5.22	perl/5.22	None	application	perl	The Perl Programming Language
perl	5.26.2	perl/5.26	None	application	perl	The Perl Programming Language
perl-mongodb	1.2.2	perl-mongodb/1.2	None	application	Utility	This is the official Perl driver for MongoDB.
perl-pcap	3.5.2	perl-pcap/3.5	None	application	computational biology	NGS reference implementations and helper code for the IGCG/TCGA Pan-Cancer Analysis Project
petsc	3.15	petsc/3.15	compiler/gcc/10:openmpi/4.0 compiler/intel/20:openmpi/4.0 compiler/intel/20:openmpi/4.1	library	runtime support
petsc	3.17	petsc/3.17	compiler/gcc/10:openmpi/4.0	library	runtime support
phast	1.5	phast/1.5	None	application	bioinformatics	PHAST is a freely available software package for comparative and evolutionary genomics.
phdf5	1.12.0	phdf5/1.12	compiler/gcc/9:openmpi/4.0 compiler/intel/19:openmpi/4.1 compiler/intel/20:openmpi/4.1 compiler/gcc/9:openmpi/4.1 compiler/gcc/10:openmpi/4.0 compiler/intel/19:openmpi/4.0 compiler/intel/20:openmpi/4.0 compiler/gcc/10:openmpi/4.1	library	runtime support
phdf5	1.14.6	phdf5/1.14	compiler/intel/2024:openmpi/4.1 compiler/intel/20:openmpi/4.1 compiler/gcc/11:openmpi/4.0 compiler/intel/19:openmpi/4.1 compiler/gcc/11:openmpi/4.1 compiler/gcc/10:openmpi/4.1 compiler/gcc/9:openmpi/4.1 compiler/pgi/20:openmpi/4.0	library	runtime support
phenix	1.18.2	phenix/1.18	compiler/gcc/9	library	runtime support
phenix	1.19.2	phenix/1.19	compiler/gcc/9	library	runtime support
phenix	1.21.2	phenix/1.21	compiler/gcc/9	library	runtime support
phist	1.0.0	phist/1.0	None	application	computational biology	Phage-Host Interaction Search Tool.
phobius	1.01	phobius/1.01	None	application	computational biology	Phobius is a combined transmembrane topology and signal peptide predictor.
phono3py	1.18.1+3	phono3py/py27/1.18	None	application	Simulation	A simulation package of phonon-phonon interaction related properties
phono3py	1.18.1+3	phono3py/py36/1.18	None	application	Simulation	A simulation package of phonon-phonon interaction related properties
phono3py	1.18.1+3	phono3py/py37/1.18	None	application	Simulation	A simulation package of phonon-phonon interaction related properties
phono3py	2.1.0	phono3py/py38/2.1	None	application	Simulation	A simulation package of phonon-phonon interaction related properties
phono3py	2.1.0	phono3py/py39/2.1	None	application	Simulation	A simulation package of phonon-phonon interaction related properties
phonopy	1.11.12	phonopy/1.11	None	library	runtime support
phonopy	2.11.0	phonopy/py37/2.11	None	library	runtime support
phonopy	2.11.0	phonopy/py39/2.11	None	library	runtime support
phylip	3.697	phylip/3.6	None	library	runtime support
phyloflash	3.4	phyloflash/3.4	None	application	Phylogeny	phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
phylogenetics	0.5.0	phylogenetics/0.5	None	application	computational biology	Python API for managing a phylogenetics projects.
phylophlan	1.0	phylophlan/1.0	None	application	computational biology	Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
phylophlan	3.0.2	phylophlan/3.0	None	application	computational biology	Precise phylogenetic analysis of microbial isolates and genomes from metagenomes
phylosnp	1.0	phylosnp/1.0	None	application	computational biology	PhyloSNP is designed to take SNP data files (.csv and .vcf) and generate phylogenetic trees from the provided data.
phyluce	1.6.8	phyluce/1.6	None	application	Genome reduction	Software for UCE (and general) phylogenomics, and it is a software package that was initially developed for analyzing data collected from ultraconserved elements in organismal genomes.
phyml	3.3.20180621	phyml/3.3	None	application	Biology	Phylogenetic estimation using (Maximum) Likelihood
picard	1.139	picard/1.1	None	application	computational biology	A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
picard	2.13	picard/2.13	None	application	computational biology	A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
picard	2.18.4	picard/2.18	None	application	computational biology	A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
picard	2.22.2	picard/2.22	None	application	computational biology	A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
picard	2.9.0	picard/2.9	None	application	computational biology	A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
picard	3.0.0	picard/3.0	None	application	computational biology	A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
picrust	1.1.0	picrust/1.1	None	application	metagenomic	The PICRUSt project aims to support prediction of the unobserved character states in a community of organisms from phylogenetic information about the organisms in that community.
picrust2	2.2.0_b	picrust2/2.2	None	application	Pipeline	PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
picrust2	2.4.1	picrust2/2.4	None	application	Pipeline	PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
picrust2	2.5.2	picrust2/2.5	None	application	Pipeline	PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
pilon	1.23	pilon/1.23	None	application	bioinformatics	Pilon is an automated genome assembly improvement and variant detection tool.
pilon	1.24	pilon/1.24	None	application	bioinformatics	Pilon is an automated genome assembly improvement and variant detection tool.
pindel	0.2.5b9	pindel/0.2	None	application	computational biology
pirs	2.0.2	pirs/2.0	None	application	computational biology
plasmidfinder	2.0.1	plasmidfinder/2.0	None	application	computational biology	PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria.
plasmidfinder	2.1	plasmidfinder/2.1	None	application	computational biology	PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria.
plink	1.90b4	plink/1.90	None	application	computational biology	PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
plink2	2.0a1	plink2/2.0a1	None	application	computational biology	This is a comprehensive update to Shaun Purcell's PLINK command-line program, developed by Christopher Chang with support from the NIH-NIDDK's Laboratory of Biological Modeling, the Purcell Lab at Mount Sinai School of Medicine, and others.
plinkseq	0.10	plinkseq/0.10	None	application	computational biology	PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data.
plumed	2.8.0	plumed/2.8	compiler/gcc/10:openmpi/4.1	application	molecular dynamics	The community-developed PLUgin for MolEcular Dynamics.
plumed	2.8.1	plumed/2.8	compiler/gcc/11:openmpi/4.1 compiler/intel/20:openmpi/4.1	application	molecular dynamics	The community-developed PLUgin for MolEcular Dynamics.
plumed	2.9.0	plumed/2.9	compiler/intel/20:openmpi/4.1 compiler/gcc/11:openmpi/4.1	application	molecular dynamics	The community-developed PLUgin for MolEcular Dynamics.
pmlst	2.0.3	pmlst/2.0	None	application	Bioinformatics	Plasmid Multi-Locus Sequence Typing
pomoxis	0.1.7	pomoxis/0.1	None	application	computational biology	Assembly, consensensus, and analysis tools by ONT research
pomoxis	0.3.13	pomoxis/0.3	None	application	computational biology	Assembly, consensensus, and analysis tools by ONT research
poplddecay	3.42	poplddecay/3.42	None	application	computational biology	Fast and effective tool for linkage disequilibrium decay analysis.
popoolation2	1.201	popoolation2/1.201	None	application	Genomics	PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences.
poppunk	1.1.6	poppunk/1.1	None	application	computational biology	PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
postgresql	15.2	postgresql/15.2	None	application	database	PostgreSQL is a powerful, open source object-relational database system.
povray	3.7.0.8	povray/3.7	None	application	CGI	The Persistence of Vision Raytracer.
pplacer	1.1	pplacer/1.1	None	application	computational biology	Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.
prank	v.170427	prank/170427	None	application	bioinformatics	PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences.
presto	0.7.2	presto/py37/0.7	None	application	computational biology	A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
primer3	2.3.7	primer3/2.3	None	application	computational biology	Primer3 picks primers for PCR reactions
prinseq-lite	0.20.4	prinseq-lite/0.20	None	application	computational biology	PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data
prodigal	2.6.3	prodigal/2.6	None	application	computational biology	Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
prodigal	2.60	prodigal/2.60	None	application	computational biology	Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
prohlatype	0.9.0	prohlatype/0.9	None	application	Computational Biology	This project provides a set of tools to calculate the full posterior distribution of HLA types given read data.
proj	7.1.1	proj/7.1	compiler/gcc/10 compiler/pgi/20 compiler/gcc/9 compiler/intel/19 compiler/intel/20	library	runtime support
prokka	1.12	prokka/1.12	None	application	bioinformatics	Prokka is a software tool for the rapid annotation of prokaryotic genomes.
prokka	1.13.7	prokka/1.13	None	application	bioinformatics	Prokka is a software tool for the rapid annotation of prokaryotic genomes.
prokka	1.14.6	prokka/1.14	None	application	bioinformatics	Prokka is a software tool for the rapid annotation of prokaryotic genomes.
proteowizard	3_0_9992	proteowizard/3.0	None	application	computational biology	ProteoWizard provides a modular and extensible set of open-source, cross-platform tools and libraries.
provean	1.1.5	provean/1.1	None	application	computational biology	PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.
psi4	1.9.1	psi4/py310/1.9	None	application	quantum chemistry	Open-Source Quantum Chemistry - an electronic structure package in C++ driven by Python
psi4	1.9.1	psi4/py311/1.9	None	application	quantum chemistry	Open-Source Quantum Chemistry - an electronic structure package in C++ driven by Python
pullseq	1.0	pullseq/1.0	None	application	computational biology	pullseq - Software to extract sequence from a fasta or fastq. Also filter sequences by a minimum length or maximum length.
purge_dups	1.2.6	purge_dups/1.2	None	application	Biology	Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth
pwtools	1.2.2	pwtools/py37/1.2	None	application	python	pwtools is a Python package for pre- and postprocessing of atomistic calculations, mostly targeted to Quantum Espresso, CPMD, CP2K and LAMMPS.
pwtools	1.2.2	pwtools/py39/1.2	None	application	python	pwtools is a Python package for pre- and postprocessing of atomistic calculations, mostly targeted to Quantum Espresso, CPMD, CP2K and LAMMPS.
pyani	0.2.11	pyani/py39/0.2	None	application	computational biology	pyani provides a package and script for calculation of genome-scale average nucleotide identity.
pyclone	0.13	pyclone/0.13	None	application	computational biology	PyClone is statistical model and software tool designed to infer the prevalence of point mutations in heterogeneous cancer samples.
pydeface	2.0.2	pydeface/2.0	None	application	neuroimaging	A tool to remove facial structure from MRI images.
pyfasta	0.5	pyfasta/0.5	None	application	computational biology	Pyfasta - fast, memory-efficient, pythonic (and command-line) access to fasta sequence files.
pygenometracks	2.0	pygenometracks/2.0	None	application	bioinformatics	Standalone program and library to plot beautiful genome browser tracks.
pyicoteo	2.0.7	pyicoteo/2.0	None	application	Biology	Analysis and manipulation of mapped reads coming from High Throughput Sequencing tool and library.
pymagic	0.1	pymagic/0.1	None	application	computational biology	MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data.
pymatgen	2023.6.28	pymatgen/py39/2023.6.28	None	application	materials analysis	Python Materials Genomics is an analysis code for materials science.
pymatgen	2023.6.28	pymatgen/py310/2023.6.28	None	application	materials analysis	Python Materials Genomics is an analysis code for materials science.
pymatgen	2023.6.28	pymatgen/py311/2023.6.28	None	application	materials analysis	Python Materials Genomics is an analysis code for materials science.
pymeteo	0.5	pymeteo/0.5	None	application	geoscience	General meteorological routines, skew-T/log-p plotting and working with CM1 model data.
pymlst	0.0.2020.06.19	pymlst/2020.06.19	None	application	computational biology	python Mlst Local Search Tool
pymol-open-source	2.4.0	pymol-open-source/py37/2.4	None	application	Molecular Dynamics	A user-sponsored molecular visualization system
pymol-open-source	2.4.0	pymol-open-source/py38/2.4	None	application	Molecular Dynamics	A user-sponsored molecular visualization system
pymol-open-source	2.4.0	pymol-open-source/py39/2.4	None	application	Molecular Dynamics	A user-sponsored molecular visualization system
pymol-open-source	2.5.0	pymol-open-source/py39/2.5	None	application	Molecular Dynamics	A user-sponsored molecular visualization system
pymol-open-source	2.5.0	pymol-open-source/py310/2.5	None	application	Molecular Dynamics	A user-sponsored molecular visualization system
pymol-open-source	2.5.0	pymol-open-source/py311/2.5	None	application	Molecular Dynamics	A user-sponsored molecular visualization system
pymongo	3.0.3	pymongo/3.0	None	application	Utility	PyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python.
pymongo	3.3.0	pymongo/3.3	None	application	Utility	PyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python.
pymongo	3.7.2	pymongo/3.7	None	application	Utility	PyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python.
pysam	0.16.0.1	pysam/py37/0.16	None	application	bioinformatics	Pysam is a python module for reading and manipulating Samfiles.
pysam	0.16.0.1	pysam/py38/0.16	None	application	bioinformatics	Pysam is a python module for reading and manipulating Samfiles.
pyseer	1.2.0	pyseer/1.2	None	application	computational biology	Sequence Elements Enrichment Analysis (SEER), python implementation
pyseer	1.3.4	pyseer/1.3	None	application	computational biology	Sequence Elements Enrichment Analysis (SEER), python implementation
python	2.7	python/2.7	None	application	system
python	3.10	python/3.10	None	application	system
python	3.11	python/3.11	None	application	system
python	3.3	python/3.3	None	application	system
python	3.4	python/3.4	None	application	system
python	3.5	python/3.5	None	application	system
python	3.6	python/3.6	None	application	system
python	3.7	python/3.7	None	application	system
python	3.8	python/3.8	None	application	system
python	3.9	python/3.9	None	application	system
python-openstackclient	2.1.0	python-openstackclient/2.1	None	application	Utility	Client for OpenStack services
python-openstackclient	6.0.0	python-openstackclient/6.0	None	application	Utility	Client for OpenStack services
pytorch	0.4.1	pytorch/py27/0.4	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	0.4.1	pytorch/py35/0.4	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	0.4.1	pytorch/py36/0.4	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.10.0	pytorch/py38/1.10	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.10.0	pytorch/py39/1.10	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.12.1	pytorch/py38/1.12	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.12.1	pytorch/py39/1.12	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.13.0	pytorch/py39/1.13	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.13.0	pytorch/py310/1.13	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.2.0	pytorch/py27/1.2	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.2.0	pytorch/py36/1.2	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.2.0	pytorch/py37/1.2	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.5.1	pytorch/py37/1.5	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.6.0	pytorch/py37/1.6	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.7.1	pytorch/py37/1.7	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.7.1	pytorch/py38/1.7	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.8.0	pytorch/py37/1.8	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.8.0	pytorch/py38/1.8	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	1.8.0	pytorch/py39/1.8	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	2.0.0	pytorch/py310/2.0	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	2.0.0	pytorch/py311/2.0	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	2.3.1	pytorch/py39/2.3	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	2.3.1	pytorch/py311/2.3	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	2.5.1	pytorch/py39/2.5	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	2.5.1	pytorch/py310/2.5	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	2.5.1	pytorch/py311/2.5	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch	2.5.1	pytorch/py312/2.5	None	application	deep learning	PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch-gpu	1.10.0	pytorch-gpu/py38/1.10	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu	1.10.0	pytorch-gpu/py39/1.10	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu	1.12.1	pytorch-gpu/py38/1.12	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu	1.12.1	pytorch-gpu/py39/1.12	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu	1.13.0	pytorch-gpu/py39/1.13	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu	1.13.0	pytorch-gpu/py310/1.13	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu	1.8.0	pytorch-gpu/py38/1.8	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu	1.9.0	pytorch-gpu/py38/1.9	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu	2.0.0	pytorch-gpu/py310/2.0	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu	2.0.0	pytorch-gpu/py311/2.0	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu	2.3.1	pytorch-gpu/py39/2.3	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu	2.3.1	pytorch-gpu/py311/2.3	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu	2.5.1	pytorch-gpu/py39/2.5	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu	2.5.1	pytorch-gpu/py310/2.5	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu	2.5.1	pytorch-gpu/py311/2.5	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
pytorch-gpu	2.5.1	pytorch-gpu/py312/2.5	None	application	deep learning	Tensors and Dynamic neural networks in Python with strong GPU acceleration
qctool	1.4	qctool/1.4	None	application	computational biology	QCTOOL is a command-line utility program for basic quality control of gwas datasets.
qgis	3.18.3	qgis/3.18	None	application	geographic information system	A free and open source Geographic Information System (GIS).
qgis	3.30.2	qgis/3.30	None	application	geographic information system	A free and open source Geographic Information System (GIS).
qgrs-cpp	2017.08.25	qgrs-cpp/2017.08.25	None	application	computational biology	C++ implementation of QGRS mapping.
qiime	1.9.1	qiime/1.9	None	application	computational biology	QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime	2017.9	qiime/2.0	None	application	computational biology	QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2	2017.9	qiime2/2017.9	None	application	computational biology	QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2	2018.2	qiime2/2018.2	None	application	computational biology	QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2	2018.4	qiime2/2018.4	None	application	computational biology	QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2	2019.1	qiime2/2019.1	None	application	computational biology	QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2	2019.10	qiime2/2019.10	None	application	computational biology	QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2	2020.2.0	qiime2/2020.2	None	application	computational biology	QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2	2021.11.0	qiime2/2021.11	None	application	computational biology	QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2	2021.2	qiime2/2021.2	None	application	computational biology	QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2	2021.4.0	qiime2/2021.4	None	application	computational biology	QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2	2022.2.0	qiime2/2022.2	None	application	computational biology	QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2	2024.10.0	qiime2/2024.10	None	application	computational biology	QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2	2024.5.0	qiime2/2024.5	None	application	computational biology	QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qmpy	1.4.0	qmpy/py36/1.4	None	application	Physics	A suite of computational materials science tools.
qmpy	1.4.0	qmpy/py37/1.4	None	application	Physics	A suite of computational materials science tools.
qmpy	1.4.0	qmpy/py38/1.4	None	application	Physics	A suite of computational materials science tools.
quake	0.3.5	quake/0.3	None	application	computational biology	Quake is a package to correct substitution sequencing errors in experiments with deep coverage.
qualimap	2.3	qualimap/2.3	None	application	sequencing alignment	Quality control of alignment sequencing data and its derivatives like feature counts
quasr	6.09	quasr/6.09	None	application	computational biology	QUASR is lightweight pipeline for processing and analysis of high-throughput sequencing data.
quast	4.1	quast/4.1	None	application	computational biology	QUAST evaluates genome assemblies by computing various metrics.
quast	4.4	quast/4.4	None	application	computational biology	QUAST evaluates genome assemblies by computing various metrics.
quast	4.5	quast/4.5	None	application	computational biology	QUAST evaluates genome assemblies by computing various metrics.
quast	5.0	quast/5.0	None	application	computational biology	QUAST evaluates genome assemblies by computing various metrics.
qupath	0.5.1	qupath/0.5	None	application	bioimaging	QuPath is open source software for bioimage analysis.
r-asreml	4.1	r-asreml/r36/4.1	None	application	data analysis	ASReml-R is a statistical package that fits linear mixed models using Residual Maximum Likelihood (REML) in the R environment.
r-asreml	4.1	r-asreml/r40/4.1	None	application	data analysis	ASReml-R is a statistical package that fits linear mixed models using Residual Maximum Likelihood (REML) in the R environment.
r-asreml	4.2	r-asreml/r43/4.2	None	application	data analysis	ASReml-R is a statistical package that fits linear mixed models using Residual Maximum Likelihood (REML) in the R environment.
r-fastbaps	1.0.1	r-fastbaps/r36/1.0	None	application	computational biology	A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
r-fastbaps	1.0.6	r-fastbaps/r41/1.0	None	application	computational biology	A fast approximation to a Dirichlet Process Mixture model (DPM) for clustering genetic data
r-genometricorr	1.1.17	r-genometricorr/r33/1.1	None	application	Genomics	Genometric Correlation (GenometriCorr) is an R package for spatial correlation of genome-wide interval datasets.
r-ggfortify	0.4.1	r-ggfortify/r33/0.4	None	application	r	ggfortify is a package of unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis.
r-hmisc	4.6_0	r-hmisc/4.6	None	application	statistics	Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, and recoding variables.
r-inla	20.03.17	r-inla/r36/20.03.17	None	application	Mathematics	Full Bayesian Analysis of Latent Gaussian Models using Integrated Nested Laplace Approximations
r-keras	2.2.4.1	r-keras/r35/2.2	None	application	machine learning	Interface to 'Keras' , a high-level neural networks 'API'.
r-markdown	0.8	r-markdown/r34/0.8	None	application	R	Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats.
r-matlib	0.9.2	r-matlib/r36/0.9	None	application	R	A collection of matrix functions for teaching and learning matrix linear algebra as used in multivariate statistical methods.
r-regresshaplo	1.0	r-regresshaplo/r34/1.0	None	application	biology	This package reconstructs haplotypes from a BAM file using a penalized regression approach.
r-rhierbaps	1.1.2	r-rhierbaps/r35/1.1	None	application	computational biology	rhierbaps is R implementation of hierBAPS.
r-rrblup	4.6.1	r-rrblup/r41/4.6	None	application	genomics	Software for genomic prediction with the RR-BLUP mixed model.
r-scimpute	0.0.5	r-scimpute/0.0.5	None	application	biology	scImpute is accurate and robust imputation of single-cell RNA sequencing data.
r-scimpute	0.0.6	r-scimpute/r34/0.0.6	None	application	biology	scImpute is accurate and robust imputation of single-cell RNA sequencing data.
r-seqminer	6.0	r-seqminer/r34/6.0	None	application	biology	SEQMINER is for sequencing variant annotation, data integration and query in R.
r-seurat	4.1.0	r-seurat/r41/4.1	None	application	computational biology	A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data.
r-vcfr	1.5.0	r-vcfr/r34/1.5	None	application	biology	A package to manipulate and visualize VCF data in R.
racon	1.5.0	racon/1.5	None	application	bioinformatics	Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
rarefactionanalyzer	2018.09.06	rarefactionanalyzer/2018.09.06	None	application	computational biology	Rarefaction analyzer is a simple program that can be used to perform rarefaction analysis.
raxml	8.2.12	raxml/8.2	None	application	Biology	Phylogenetics - Randomized Axelerated Maximum Likelihood.
raxml-ng	1.0.3	raxml-ng/1.0	compiler/gcc/10:openmpi/4.1	application	Genetics	RAxML Next Generation: faster, easier-to-use and more flexible
raxml-ng	1.1.0	raxml-ng/1.1	compiler/gcc/10:openmpi/4.1	application	Genetics	RAxML Next Generation: faster, easier-to-use and more flexible
raxml-ng	1.2.0	raxml-ng/1.2	compiler/gcc/10:openmpi/4.1	application	Genetics	RAxML Next Generation: faster, easier-to-use and more flexible
ray	2.3.1	ray/2.3	None	application	computational biology	Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data.
rclone	1.44	rclone/1.44	None	application	Storage	Rclone ("rsync for cloud storage") is a command line program to sync files and directories to and from different cloud storage providers.
rclone	1.50.2	rclone/1.50	None	application	Storage	Rclone ("rsync for cloud storage") is a command line program to sync files and directories to and from different cloud storage providers.
rclone	1.51.0	rclone/1.51	None	application	Storage	Rclone ("rsync for cloud storage") is a command line program to sync files and directories to and from different cloud storage providers.
rclone	1.59.2	rclone/1.59	None	application	Storage	Rclone ("rsync for cloud storage") is a command line program to sync files and directories to and from different cloud storage providers.
rclone	1.64.2	rclone/1.64	None	application	Storage	Rclone ("rsync for cloud storage") is a command line program to sync files and directories to and from different cloud storage providers.
read2tree	0.1.5	read2tree/py39/0.1	None	application	computational biology	Building phylogenetic trees directly from sequencing reads
read2tree	0.1.5	read2tree/py310/0.1	None	application	computational biology	Building phylogenetic trees directly from sequencing reads
readosm	1.1	readosm/1.1	compiler/gcc/9	unknown	unknown
readosm	1.1.0a	readosm/1.1	compiler/intel/20 compiler/intel/19 compiler/gcc/10	unknown	unknown
reago	1.1	reago/1.1	None	application	bioinformatics	Reconstructing 16S rRNA genes in metagenomic data.
red	2015.05.22	red/2015.05.22	None	application	Genomics	Red (RepeatsDetector): an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.
regtools	0.5.0	regtools/0.5	None	application	bioinformatics	Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
relion	4.0.0	relion/4.0	compiler/intel/20:openmpi/4.1	application	Physics
relion-gpu	4.0.0	relion-gpu/4.0	compiler/gcc/11:openmpi/4.1	application	Physics
repeatmasker	4.0	repeatmasker/4.0	None	application	computational biology	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
repenrich	1.2	repenrich/1.2	None	application	computational biology	RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.
resfinder	4.1.11	resfinder/4.1	None	application	unknown	ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria.
resistomeanalyzer	2018.09.06	resistomeanalyzer/2018.09.06	None	application	computational biology	Resistome Analyzer is a simple tool for analyzing the resistome of large metagenomic datasets.
retroseq	1.5	retroseq/1.5	None	application	bioinformatics	RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements.
revbayes	1.2.2	revbayes/1.2	compiler/gcc/11:openmpi/4.1	application	Bioinformatics	Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.
revtrans	1.4	revtrans/1.4	None	application	computational biology	RevTrans - performs a reverse translation of a peptide alignment.
rgi	5.1.0	rgi/5.1	None	application	computational biology	Resistance gene identifier.
rgi	5.2.1	rgi/5.2	None	application	computational biology	Resistance gene identifier.
rgi	6.0.2	rgi/6.0	None	application	computational biology	Resistance gene identifier.
rgt	0.11.4	rgt/0.11	None	application	computational biology	Toolkit to perform regulatory genomics data analysis
ripgrep	13.0.0	ripgrep/13.0	None	application	Utility	ripgrep recursively searches directories for a regex pattern
ripser	1.0.1	ripser/1.0	None	application	Bioinformatics	Ripser: efficient computation of Vietoris–Rips persistence barcodes.
rmats	4.1.2	rmats/4.1	None	application	computational biology	MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data.
rmats	4.3.0	rmats/4.3	None	application	computational biology	MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data.
rnaclust	1.3	rnaclust/1.3	None	application	computational biology	A tool for clustering of RNAs based on their secondary structures using LocARNA
rnahybrid	2.1.2	rnahybrid/2.1	None	application	computational biology	RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA.
rnammer	1.2	rnammer/1.2	None	application	computational biology	RNAmmer predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.
rnaquast	1.5.1	rnaquast/1.5	None	application	Biology	rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.
rnasnp	1.2	rnasnp/1.2	None	application	computational biology	Efficient detection of local RNA secondary structure changes induced by SNPs.
rnastructure	6.1	rnastructure/6.1	None	application	Bioinformatics	RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data.
roary	3.12.0	roary/3.12	None	application	computational biology	Rapid large-scale prokaryote pan genome analysis
roary	3.13.0	roary/3.13	None	application	computational biology	Rapid large-scale prokaryote pan genome analysis
rosetta	3.12	rosetta/3.12	compiler/gcc/9:openmpi/4.1	application	computational biology	The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.
rosetta	3.13	rosetta/3.13	compiler/gcc/9:openmpi/4.1	application	computational biology	The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.
rosettafold	1.0.0	rosettafold/1.0	None	application	bioinformatics	RoseTTAFold - Accurate prediction of protein structures and interactions using a 3-track network.
rosettafold2na	0.2	rosettafold2na/0.2	None	application	computational biology	RoseTTAFold2 protein/nucleic acid complex prediction.
rsem	1.2	rsem/1.2	None	application	computational biology	RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
rsem	1.3	rsem/1.3	None	application	computational biology	RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
rstudio	2023.12	rstudio/2023.12	None	library	runtime support	RStudio is an integrated development environment (IDE) for R and Python.
rsync	3.1.3	rsync/3.1	None	application	System	Tool for fast incremental file transfer
rsync	3.2.3	rsync/3.2	None	application	System	Tool for fast incremental file transfer
ruby	2.1	ruby/2.1	None	application	programming language	A dynamic, open source programming language with a focus on simplicity and productivity.
ruby	3.4.1	ruby/3.4	None	application	programming language	A dynamic, open source programming language with a focus on simplicity and productivity.
rucs	1.0.2	rucs/1.0	None	application	computational biology	RUCS is a bioinformatics tool developed to ease the task of designing new primers.
rust	1.41.0	rust/1.41	None	application	System	Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. This package provides the compiler (rustc) and the documentation utilities rustdoc.
saga-gis	2.3	saga-gis/py27/2.3	None	application	Geoscience	SAGA - System for Automated Geoscience Analysis.
saga-gis	8.3.1	saga-gis/py37/8.3	None	application	Geoscience	SAGA - System for Automated Geoscience Analysis.
saga-gis	8.3.1	saga-gis/py38/8.3	None	application	Geoscience	SAGA - System for Automated Geoscience Analysis.
saga-gis	8.3.1	saga-gis/py39/8.3	None	application	Geoscience	SAGA - System for Automated Geoscience Analysis.
sage	10.4	sage/10.4	None	application	mathematics	Sage - Open Source Mathematical Software.
sage	6.3	sage/6.3	None	application	mathematics	Sage - Open Source Mathematical Software.
salmon	0.6.0	salmon/0.6	None	application	computational biology	Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.
salmon	0.8.2	salmon/0.8	None	application	computational biology	Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.
salmon	0.9.1	salmon/0.9	None	application	computational biology	Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.
salmon	1.4.0	salmon/1.4	None	application	computational biology	Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.
salsa2	2.3	salsa2/2.3	None	application	bioinformatics	Salsa is a tool to scaffold long read assemblies with Hi-C.
sambamba	0.8.1	sambamba/0.8	None	application	Bioinformatics	Tools for working with SAM/BAM data
samblaster	0.1.26	samblaster/0.1	None	application	computational biology	Mark duplicates in and extract discordant and split reads from SAM files.
samrai	2.4	samrai/2.4	compiler/gcc/10:openmpi/4.0	library	numerical
samtools	0.1	samtools/0.1	None	application	computational biology	Tools for dealing with SAM, BAM and CRAM files
samtools	1.15.1	samtools/1.15	None	application	computational biology	Tools for dealing with SAM, BAM and CRAM files
samtools	1.17	samtools/1.17	None	application	computational biology	Tools for dealing with SAM, BAM and CRAM files
samtools	1.19	samtools/1.19	None	application	computational biology	Tools for dealing with SAM, BAM and CRAM files
samtools	1.20	samtools/1.20	None	application	computational biology	Tools for dealing with SAM, BAM and CRAM files
samtools	1.3	samtools/1.3	None	application	computational biology	Tools for dealing with SAM, BAM and CRAM files
samtools	1.5	samtools/1.5	None	application	computational biology	Tools for dealing with SAM, BAM and CRAM files
samtools	1.6	samtools/1.6	None	application	computational biology	Tools for dealing with SAM, BAM and CRAM files
samtools	1.9	samtools/1.9	None	application	computational biology	Tools for dealing with SAM, BAM and CRAM files
sas	9.4	sas/9.4	None	application	Applications	SAS is a software suite developed by SAS Institute for advanced analytics, business intelligence, data management, and predictive analytics.
scaffold_builder	2.2	scaffold_builder/2.2	None	application	computational biology	Scaffold_builder: Combining de novo and reference-guided assembly with Scaffold_builder.
scan-for-matches	1.0	scan-for-matches/1.0	None	application	computational biology	scan_for_matches is a utility written in C for locating patterns in DNA or protein FASTA files.
schrodinger	2020.1	schrodinger/2020.1	None	application	Simulation	Schrödinger is the scientific leader in developing state-of-the-art chemical simulation software for use in pharmaceutical, biotechnology, and materials research.
schrodinger	2020.4	schrodinger/2020.4	None	application	Simulation	Schrödinger is the scientific leader in developing state-of-the-art chemical simulation software for use in pharmaceutical, biotechnology, and materials research.
schrodinger	2021.1	schrodinger/2021.1	None	application	Simulation	Schrödinger is the scientific leader in developing state-of-the-art chemical simulation software for use in pharmaceutical, biotechnology, and materials research.
schrodinger	2022.1	schrodinger/2022.1	None	application	Simulation	Schrödinger is the scientific leader in developing state-of-the-art chemical simulation software for use in pharmaceutical, biotechnology, and materials research.
scip	4.0.0	scip/4.0	None	application	constraint integer programming	SCIP is currently one of the fastest non-commercial solvers for mixed integer programming (MIP) and mixed integer nonlinear programming (MINLP).
scoary	1.6.16	scoary/py27/1.6	None	application	computational biology	Microbial pan-GWAS using the output from Roary
scoary	1.6.16	scoary/py35/1.6	None	application	computational biology	Microbial pan-GWAS using the output from Roary
scoary	1.6.16	scoary/py36/1.6	None	application	computational biology	Microbial pan-GWAS using the output from Roary
scons	2.5	scons/2.5	None	application	utility	SCons: A software construction tool.
scons	3.0	scons/3.0	None	application	utility	SCons: A software construction tool.
scons	3.1.2	scons/py27/3.1	None	application	utility	SCons: A software construction tool.
scons	3.1.2	scons/py38/3.1	None	application	utility	SCons: A software construction tool.
scons	3.1.2	scons/py39/3.1	None	application	utility	SCons: A software construction tool.
scons	4.2.0	scons/py37/4.2	None	application	utility	SCons: A software construction tool.
scons	4.2.0	scons/py38/4.2	None	application	utility	SCons: A software construction tool.
scons	4.2.0	scons/py39/4.2	None	application	utility	SCons: A software construction tool.
scons	4.3.0	scons/py37/4.3	None	application	utility	SCons: A software construction tool.
scons	4.3.0	scons/py38/4.3	None	application	utility	SCons: A software construction tool.
scons	4.3.0	scons/py39/4.3	None	application	utility	SCons: A software construction tool.
scythe	0.991	scythe/0.991	None	application	bioinformatics	A 3'-end adapter contaminant trimmer.
seacr	1.3	seacr/1.3	None	application	computational biology	SEACR is Sparse Enrichment Analysis for CUT&RUN
seedme	1.2	seedme/1.2	None	application	Utility	Client program for SeedMe.org.
selecton	2.4	selecton/2.4	None	application	Bioinformatics	Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach.
sepp	1.0	sepp/1.0	None	library	runtime support
seqkit	0.10.1	seqkit/0.10	None	application	computational biology	Cross-platform and ultrafast toolkit for FASTA/Q file manipulation
seqkit	2.6.1	seqkit/2.6	None	application	computational biology	Cross-platform and ultrafast toolkit for FASTA/Q file manipulation
seqtk	1.2	seqtk/1.2	None	application	computational biology	Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format.
sequeltools	2021.05.18	sequeltools/2021.05.18	None	application	bioinformatics	A suite of tools for working with PacBio Sequel raw sequence data.
sequencetubemap	2025.01.28	sequencetubemap/2025.01.28	None	application	genomics	Displays multiple genomic sequences in the form of a tube map.
seqyclean	1.10.07	seqyclean/1.10	None	application	Bioinformatics	Main purpose of this software is to pre-process NGS data in order to prepare for downstream analysis.
settarg	None	settarg	None	unknown	unknown	The settarg module provides a way to connect the loaded modules with your build system by setting environment variables.
settarg	settarg	settarg/settarg	None	unknown	unknown	The settarg module provides a way to connect the loaded modules with your build system by setting environment variables.
sff2fastq	0.9.2	sff2fastq/0.9	None	application	computational biology	The program sff2fastq extracts read information from a SFF file, produced by the 454 genome sequencer, and outputs the sequences and quality scores in a FASTQ format.
shapeit	2.0	shapeit/2.0	None	application	computational biology	SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.
shapeit	5.1.1	shapeit/5.1	None	application	computational biology	SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.
shapelib	1.5.0	shapelib/1.5	compiler/intel/19 compiler/gcc/10 compiler/intel/20 compiler/pgi/20 compiler/gcc/9	library	runtime support	The Shapefile C Library provides the ability to write simple C programs for reading, writing and updating (to a limited extent) ESRI Shapefiles, and the associated attribute file (.dbf).
shasta	0.11.1	shasta/0.11	None	application	Bioinformatics	De novo assembly from Oxford Nanopore reads.
shasta	0.8.0	shasta/0.8	None	application	Bioinformatics	De novo assembly from Oxford Nanopore reads.
shortbred	0.9.5	shortbred/0.9	None	application	bioinformatics	ShortBRED is a system for profiling protein families of interest at very high specificity in shotgun metagenomic sequencing data.
shortstack	3.8.5	shortstack/3.8	None	application	Biology	ShortStack: Comprehensive annotation and quantification of small RNA genes
shovill	1.0.9	shovill/1.0	None	application	computational biology	Microbial assembly pipeline for Illumina paired-end reads
shrimp	2.2	shrimp/2.2	None	application	computational biology	SHRiMP is a software package for aligning genomic reads against a target genome.
shtns	2.6.3	shtns/py36/2.6	None	application	high performance library	SHTns is a high performance library for Spherical Harmonic Transform written in C, aimed at numerical simulation (fluid flows, mhd, ...) in spherical geometries.
shtns	2.6.3	shtns/py310/2.6	None	application	high performance library	SHTns is a high performance library for Spherical Harmonic Transform written in C, aimed at numerical simulation (fluid flows, mhd, ...) in spherical geometries.
shtns	3.6	shtns/py36/3.6	None	application	high performance library	SHTns is a high performance library for Spherical Harmonic Transform written in C, aimed at numerical simulation (fluid flows, mhd, ...) in spherical geometries.
shtns	3.6	shtns/py310/3.6	None	application	high performance library	SHTns is a high performance library for Spherical Harmonic Transform written in C, aimed at numerical simulation (fluid flows, mhd, ...) in spherical geometries.
sicerpy	0.1.1	sicerpy/0.1	None	application	Biology	Python wrapper around the popular ChIP-Seq peak caller SICER.
sickle	1.2	sickle/1.210	None	application	computational biology	A windowed adaptive trimming tool for FASTQ files using quality
sickle	1.33	sickle/1.33	None	application	computational biology	A windowed adaptive trimming tool for FASTQ files using quality
sift4g	2.0.0	sift4g/2.0	None	application	computational biology	SIFT 4G is a faster version of SIFT that enables us to scale up and provide SIFT predictions for more organisms.
signalp	4.1	signalp/4.1	None	application	Biology	signalp predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes.
signalp	5.0b	signalp/5.0b	None	application	Biology	signalp predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes.
silo	4.11	silo/4.11	compiler/gcc/10:openmpi/4.0	application	API
simrna	3.20	simrna/3.20	None	application	computational biology	SimRNA is a tool for simulations of RNA conformational dynamics
singularity	3.8	singularity/2.2	None	application	system	Application containers enabling mobility of compute.
singularity	3.8	singularity/2.3	None	application	system	Application containers enabling mobility of compute.
singularity	3.8	singularity/2.4	None	application	system	Application containers enabling mobility of compute.
singularity	3.8	singularity/2.6	None	application	system	Application containers enabling mobility of compute.
singularity	3.8	singularity/3.2	None	application	system	Application containers enabling mobility of compute.
singularity	3.8	singularity/3.8	None	application	system	Application containers enabling mobility of compute.
sistr_cmd	1.0.2	sistr_cmd/1.0	None	application	computational biology	Salmonella In Silico Typing Resource command-line tool
sistr_cmd	1.1.1	sistr_cmd/1.1	None	application	computational biology	Salmonella In Silico Typing Resource command-line tool
skewer	0.2.2	skewer/0.2	None	application	dynamic programming algorithm	A fast and accurate adapter trimmer for next-generation sequencing paired-end reads.
smetana	1.2.0	smetana/py36/1.2	None	application	genomics	Species METabolic interaction ANAlysis (SMETANA) is a python-based command line tool to analyse microbial communities.
smrtlink	10.1.0.119588	smrtlink/10.1	None	application	Biology	PacBio's open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.
smrtlink	5.0.1	smrtlink/5.0	None	application	Biology	PacBio's open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.
smrtlink	5.1.0.26412	smrtlink/5.1	None	application	Biology	PacBio's open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.
smrtlink	7.0.1.66975	smrtlink/7.0	None	application	Biology	PacBio's open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.
snakemake	5.18.0	snakemake/5.18	None	application	Utility	A popular workflow management system aiming at full in-silico reproducibility.
snakemake	6.4.1	snakemake/6.4	None	application	Utility	A popular workflow management system aiming at full in-silico reproducibility.
snakemake	8.28.0	snakemake/8.28	None	application	Utility	A popular workflow management system aiming at full in-silico reproducibility.
snap	2013-11-29	snap/2013-11-29	None	application	computational biology	SNAP - (Semi-HMM-based Nucleic Acid Parser) gene prediction tool.
sniffles	1.0.12	sniffles/1.0	None	application	computational biology	Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore)
sniffles	2.4	sniffles/2.4	None	application	computational biology	Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore)
snippy	4.3.6	snippy/4.3	None	application	computational biology	Rapid bacterial SNP calling and core genome alignments
snippy	4.6.0	snippy/4.6	None	application	computational biology	Rapid bacterial SNP calling and core genome alignments
snp-dists	0.6.3	snp-dists/0.6	None	application	computational biology	Convert a FASTA alignment to SNP distance matrix
snp-dists	0.7.0	snp-dists/0.7	None	application	computational biology	Convert a FASTA alignment to SNP distance matrix
snp-dists	0.8.2	snp-dists/0.8	None	application	computational biology	Convert a FASTA alignment to SNP distance matrix
snp-pipeline	0.6	snp-pipeline/0.6	None	application	computational biology	Script and functions for SNP matrix construction
snp-pipeline	0.7	snp-pipeline/0.7	None	application	computational biology	Script and functions for SNP matrix construction
snp-pipeline	1.0	snp-pipeline/1.0	None	application	computational biology	Script and functions for SNP matrix construction
snp-pipeline	2.0.2	snp-pipeline/2.0	None	application	computational biology	Script and functions for SNP matrix construction
snp-sites	2.3.3	snp-sites/2.3	None	application	computational biology	SNP-sites rapidly extracts SNPs from a multi-FASTA alignment.
snp-sites	2.4.1	snp-sites/2.4	None	application	computational biology	SNP-sites rapidly extracts SNPs from a multi-FASTA alignment.
snp-sites	2.5.1	snp-sites/2.5	None	application	computational biology	SNP-sites rapidly extracts SNPs from a multi-FASTA alignment.
snpeff	4.3	snpeff/4.3	None	application	computational biology	Genetic variant annotation and effect prediction toolbox.
snpeff	5.1	snpeff/5.1	None	application	computational biology	Genetic variant annotation and effect prediction toolbox.
snpfinder	1.0.0	snpfinder/1.0	None	application	computational biology	SNPFinder is a simple alignment-based haplotype variant caller that can be used with metagenomic sequence data.
snptest	2.5.2	snptest/2.5	None	application	computational biology	SNPTEST is a program for the analysis of single SNP association in genome-wide studies.
soapdenovo-trans	1.04	soapdenovo-trans/1.04	None	application	computational biology	SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.
soapdenovo2	r240	soapdenovo2/r240	None	application	computational biology	soapdenovo2 - novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes
sonnet	1.19	sonnet/py27/1.19	None	application	machine learning	Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet	1.19	sonnet/py35/1.19	None	application	machine learning	Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet	1.19	sonnet/py36/1.19	None	application	machine learning	Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet	1.23	sonnet/py27/1.23	None	application	machine learning	Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet	1.23	sonnet/py35/1.23	None	application	machine learning	Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet	1.23	sonnet/py36/1.23	None	application	machine learning	Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet	1.27	sonnet/py27/1.27	None	application	machine learning	Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet	1.27	sonnet/py36/1.27	None	application	machine learning	Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet	2.0.0	sonnet/py38/2.0	None	application	machine learning	Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet	2.0.0	sonnet/py39/2.0	None	application	machine learning	Sonnet is a library built on top of TensorFlow 2 designed to provide simple, composable abstractions for machine learning research.
sonnet-gpu	1.19	sonnet-gpu/py27/1.19	None	application	machine learning	Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet-gpu	1.19	sonnet-gpu/py35/1.19	None	application	machine learning	Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet-gpu	1.19	sonnet-gpu/py36/1.19	None	application	machine learning	Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet-gpu	1.23	sonnet-gpu/py27/1.23	None	application	machine learning	Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet-gpu	1.23	sonnet-gpu/py35/1.23	None	application	machine learning	Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet-gpu	1.23	sonnet-gpu/py36/1.23	None	application	machine learning	Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet-gpu	1.27	sonnet-gpu/py27/1.27	None	application	machine learning	Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet-gpu	1.27	sonnet-gpu/py36/1.27	None	application	machine learning	Sonnet is a library built on top of TensorFlow for building complex neural networks.
sortmerna	4.3.2	sortmerna/4.3.2	None	application	biological sequence analysis	SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads.
spacy	2.2.3	spacy/py36/2.2	None	application	deep learning	Industrial-strength Natural Language Processing
spacy	2.2.3	spacy/py37/2.2	None	application	deep learning	Industrial-strength Natural Language Processing
spacy-gpu	2.2.4	spacy-gpu/py36/2.2	None	application	deep learning	Industrial-strength Natural Language Processing
spacy-gpu	2.2.4	spacy-gpu/py37/2.2	None	application	deep learning	Industrial-strength Natural Language Processing
spades	3.10.1	spades/3.10	None	application	computational biology	SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades	3.11.1	spades/3.11	None	application	computational biology	SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades	3.12.0	spades/3.12	None	application	computational biology	SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades	3.13.0	spades/py27/3.13	None	application	computational biology	SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades	3.13.0	spades/py35/3.13	None	application	computational biology	SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades	3.13.0	spades/py36/3.13	None	application	computational biology	SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades	3.14.0	spades/3.14	None	application	computational biology	SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades	3.15.2	spades/3.15	None	application	computational biology	SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades	3.8.1	spades/3.8	None	application	computational biology	SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
sparcc	0.1.0	sparcc/py27/0.1	None	application	computational biology	SparCC is a python module for computing correlations in compositional data (16S, metagenomics, etc).
sparta	18Jul2022	sparta/18Jul2022	compiler/gcc/11:openmpi/4.1	application	Simulation	Stochastic PArallel Rarefied-gas Time-accurate Analyzer.
spglib	2.0.2	spglib/2.0	compiler/intel/20	library	runtime support
spider	2.0	spider/2.0	None	application	computational biology	Sequence-based Prediction of Local and Nonlocal Structural Features for Proteins.
spirit	2.1.1	spirit/py36/2.1	None	application	Physics	Optimizations and Dynamics Framework for atomistic Spin systems
spirit	2.1.1	spirit/py37/2.1	None	application	Physics	Optimizations and Dynamics Framework for atomistic Spin systems
spirit	2.1.1	spirit/py38/2.1	None	application	Physics	Optimizations and Dynamics Framework for atomistic Spin systems
spirit-gpu	2.1.1	spirit-gpu/py36/2.1	None	application	Physics	Optimizations and Dynamics Framework for atomistic Spin systems
spirit-gpu	2.1.1	spirit-gpu/py37/2.1	None	application	Physics	Optimizations and Dynamics Framework for atomistic Spin systems
spirit-gpu	2.1.1	spirit-gpu/py38/2.1	None	application	Physics	Optimizations and Dynamics Framework for atomistic Spin systems
spm	12	spm/12	compiler/gcc/11	application	matlab toolbox	Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data.
spp	1.11	spp/1.11	None	application	computational biology	ChIP-seq peak caller
spp	1.13	spp/1.13	None	application	computational biology	ChIP-seq peak caller
spython	0.0.69	spython/0.0.69	None	application	singularity	Command line python tool for working with singularity.
sqlite	3.33.0	sqlite/3.33	compiler/gcc/11 compiler/pgi/20 compiler/gcc/9 compiler/intel/19 compiler/gcc/10 compiler/intel/20	library	runtime support
ssages	0.9.3	ssages/0.9gromacs	compiler/gcc/9:openmpi/4.0	application	molecular dynamics
ssages	0.9.3	ssages/0.9lammps	compiler/gcc/9:openmpi/4.0	application	molecular dynamics
ssake	4.0	ssake/4.0	None	application	genomics	SSAKE is a genomics application for de novo assembly of millions of very short DNA sequences.
stacks	2.4	stacks/2.4	None	application	computational biology	Stacks is a software pipeline for building loci from RAD-seq
stacks	2.68	stacks/2.68	None	application	computational biology	Stacks is a software pipeline for building loci from RAD-seq
stamp	2.1.3	stamp/2.1	None	application	Taxonomy	A graphical software package for analyzing taxonomic and functional profiles.
staphb-toolkit	1.3.6	staphb-toolkit/1.3	None	application	Bioinformatics	The StaPH-B ToolKit is a Python library of commonly used bioinformatics tools that help to inform public health action. The StaPH-B ToolKit utilizes the StaPH-B Docker Images to enable easy access of open-source software without the need of local installation and/or dependency maintenance.
staphb-toolkit	2.0.1	staphb-toolkit/2.0	None	application	Bioinformatics	The StaPH-B ToolKit is a Python library of commonly used bioinformatics tools that help to inform public health action. The StaPH-B ToolKit utilizes the StaPH-B Docker Images to enable easy access of open-source software without the need of local installation and/or dependency maintenance.
staphb-toolkit	20200304	staphb-toolkit/20200304	None	application	Bioinformatics	The StaPH-B ToolKit is a Python library of commonly used bioinformatics tools that help to inform public health action. The StaPH-B ToolKit utilizes the StaPH-B Docker Images to enable easy access of open-source software without the need of local installation and/or dependency maintenance.
star	2.7.11b	star/2.7	None	application	biology	An RNA-seq read aligner.
star	2.7.9a	star/2.7.9a	None	application	biology	An RNA-seq read aligner.
star-fusion	1.13.0	star-fusion/1.13	None	application	computational biology	STAR-Fusion fusion variant caller.
star-fusion	1.9.0	star-fusion/1.9	None	application	computational biology	STAR-Fusion fusion variant caller.
starccm	10.01.010	starccm/10.06	None	library	runtime support
starccm	9.01.011	starccm/9.06	None	library	runtime support
starship	1.20.1	starship/1.20	None	application	Cross-shell prompt	The minimal, blazing-fast, and infinitely customizable prompt for any shell!
stereogene	2.20	stereogene/2.20	None	application	sequencing	StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data
strainest	1.2.4	strainest/1.2	None	application	Biology	Abundance estimation of strains
strelka	2.9.10	strelka/2.9	None	application	computational biology	Strelka calls somatic and germline small variants from mapped sequencing reads
stringmlst	0.6.3	stringmlst/0.6	None	application	computational biology	Fast k-mer based tool for multi locus sequence typing (MLST) directly from genome sequencing reads
structure	2.3.4	structure/2.3	None	application	computational biology	The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.
subread	1.4.6p5	subread/1.4	None	application	computational biology	The Subread package is developed in The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia. It consists of a suite of programs for processing next-gen sequencing data.
subread	2.0.0	subread/2.0	None	application	computational biology	The Subread package is developed in The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia. It consists of a suite of programs for processing next-gen sequencing data.
subversion	1.10.8	subversion/1.10	None	library	tools	Enterprise-class centralized version control for the masses
subversion	1.14.2	subversion/1.14	None	library	tools	Enterprise-class centralized version control for the masses
suitesparse	5.10.1	suitesparse/5.10	compiler/gcc/10	library	runtime support	SuiteSparse: A Suite of Sparse matrix packages.
svn	1.10.8	svn/1.10	None	library	tools	Enterprise-class centralized version control for the masses
svn	1.14.2	svn/1.14	None	library	tools	Enterprise-class centralized version control for the masses
svsolver	2022.07.20	svsolver/2022.07.20	compiler/gcc/10:openmpi/4.1	application	Biology	The svSolver includes three executable programs: Presolver(svpre), Flowsolver(svsolver), Postsolver(svpost).
swan	None	swan	None	unknown	unknown
sweepfinder2	1.0	sweepfinder2/1.0	None	application	Biology	The BWA read mapper.
szip	2.1	szip/2.1	compiler/intel/18 compiler/gcc/11 compiler/gcc/9 compiler/gcc/10	library	runtime support
szip	2.1.1	szip/2.1	compiler/pgi/20 compiler/intel/19 compiler/intel/2024 compiler/intel/20	library	runtime support
t-coffee	13.39.0.d675aed	t-coffee/13.39	None	application	computational biology	A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
t-coffee	13.45.0.4846264	t-coffee/13.45	None	application	computational biology	A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence
tabix	0.2.6	tabix/0.2	None	application	computational biology	A set of tools written in Perl and C++ for working with VCF files.
tagcleaner	0.16	tagcleaner/0.16	None	application	computational biology	The TagCleaner tool can be used to automatically detect and efficiently remove tag sequences (e.g. WTA tags) from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.
targetfinder	1.7	targetfinder/1.7	None	application	computational biology	Plant small RNA target prediction tool.
tassel	3.0	tassel/3.0	None	application	computational biology	TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
tassel	4.0	tassel/4.0	None	application	computational biology	TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
tassel	5.1	tassel/5.1	None	application	computational biology	TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
tassel	5.2.89	tassel/5.2	None	application	computational biology	TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
tax2tree	1.0	tax2tree/1.0	None	application	computational biology	tax2tree - Tools for decorating taxonomy information on to a phylogenetic tree.
taxypro	1.0	taxypro/1.0	None	application	mixture modeling for taxonomic analysis of metagenomes
taxytoolbox	1.0	taxytoolbox/1.0	None	application	mixture modeling for taxonomic analysis of metagenomes
tciaclient	0.0.3	tciaclient/py38/0.0.3	None	application	TCIA	TCIA (The Cancer Imaging Archive) Download Client for Python
tensorflow	0.12.1	tensorflow/py27/0.12	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	0.12.1	tensorflow/py35/0.12	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.0.0	tensorflow/py27/1.0	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.0.0	tensorflow/py35/1.0	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.11.0	tensorflow/py27/1.11	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.11.0	tensorflow/py36/1.11	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.12.0	tensorflow/py27/1.12	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.12.0	tensorflow/py36/1.12	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.14.0	tensorflow/py27/1.14	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.14.0	tensorflow/py36/1.14	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.14.0	tensorflow/py37/1.14	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.3.1	tensorflow/py27/1.3	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.3.1	tensorflow/py35/1.3	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.3.1	tensorflow/py36/1.3	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.4.0	tensorflow/py27/1.4	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.4.0	tensorflow/py35/1.4	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.4.0	tensorflow/py36/1.4	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.5.0	tensorflow/py27/1.5	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.5.0	tensorflow/py35/1.5	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.5.0	tensorflow/py36/1.5	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.7.0	tensorflow/py27/1.7	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.7.0	tensorflow/py35/1.7	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	1.7.0	tensorflow/py36/1.7	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.0.0	tensorflow/py36/2.0	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.0.0	tensorflow/py37/2.0	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.1.0	tensorflow/py36/2.1	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.1.0	tensorflow/py37/2.1	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.10.0	tensorflow/py38/2.10	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.10.0	tensorflow/py39/2.10	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.11.0	tensorflow/py38/2.11	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.11.0	tensorflow/py39/2.11	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.15.0	tensorflow/py310/2.15	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.15.0	tensorflow/py311/2.15	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.17.0	tensorflow/py310/2.17	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.17.0	tensorflow/py311/2.17	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.2.0	tensorflow/py36/2.2	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.2.0	tensorflow/py37/2.2	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.3.0	tensorflow/py37/2.3	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.3.0	tensorflow/py38/2.3	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.4.1	tensorflow/py37/2.4	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.4.1	tensorflow/py38/2.4	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.4.1	tensorflow/py39/2.4	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.5.0	tensorflow/py37/2.5	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.5.0	tensorflow/py38/2.5	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.5.0	tensorflow/py39/2.5	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.6.0	tensorflow/py38/2.6	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.6.0	tensorflow/py39/2.6	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.7.0	tensorflow/py38/2.7	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.7.0	tensorflow/py39/2.7	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.8.2	tensorflow/py38/2.8	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.8.2	tensorflow/py39/2.8	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.9.1	tensorflow/py38/2.9	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow	2.9.1	tensorflow/py39/2.9	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	1.12.0	tensorflow-gpu/py27/1.12	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	1.12.0	tensorflow-gpu/py36/1.12	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	1.13.1	tensorflow-gpu/py27/1.13	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	1.13.1	tensorflow-gpu/py36/1.13	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	1.13.1	tensorflow-gpu/py37/1.13	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	1.14.0	tensorflow-gpu/py27/1.14	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	1.14.0	tensorflow-gpu/py36/1.14	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	1.14.0	tensorflow-gpu/py37/1.14	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	1.5.0	tensorflow-gpu/py27/1.5	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	1.5.0	tensorflow-gpu/py35/1.5	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	1.5.0	tensorflow-gpu/py36/1.5	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	1.7.0	tensorflow-gpu/py27/1.7	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	1.7.0	tensorflow-gpu/py35/1.7	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	1.7.0	tensorflow-gpu/py36/1.7	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.0.0	tensorflow-gpu/py36/2.0	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.0.0	tensorflow-gpu/py37/2.0	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.1.0	tensorflow-gpu/py36/2.1	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.1.0	tensorflow-gpu/py37/2.1	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.10.0	tensorflow-gpu/py38/2.10	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.10.0	tensorflow-gpu/py39/2.10	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.11.0	tensorflow-gpu/py38/2.11	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.11.0	tensorflow-gpu/py39/2.11	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.15.0	tensorflow-gpu/py310/2.15	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.15.0	tensorflow-gpu/py311/2.15	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.17.0	tensorflow-gpu/py310/2.17	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.17.0	tensorflow-gpu/py311/2.17	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.2.0	tensorflow-gpu/py36/2.2	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.2.0	tensorflow-gpu/py37/2.2	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.3.0	tensorflow-gpu/py38/2.3	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.4.1	tensorflow-gpu/py38/2.4	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.4.1	tensorflow-gpu/py39/2.4	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.5.0	tensorflow-gpu/py37/2.5	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.5.0	tensorflow-gpu/py38/2.5	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.5.0	tensorflow-gpu/py39/2.5	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.6.0	tensorflow-gpu/py38/2.6	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.6.0	tensorflow-gpu/py39/2.6	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.7.0	tensorflow-gpu/py38/2.7	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.7.0	tensorflow-gpu/py39/2.7	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.8.1	tensorflow-gpu/py38/2.8	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.8.1	tensorflow-gpu/py39/2.8	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.9.1	tensorflow-gpu/py38/2.9	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	2.9.1	tensorflow-gpu/py39/2.9	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	py37/2.3	tensorflow-gpu/py37/2.3	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow-gpu	py37/2.4	tensorflow-gpu/py37/2.4	None	application	machine learning	TensorFlow is an open source software library for numerical computation using data flow graphs.
tf-comb	1.0.3	tf-comb/py38/1.0	None	application	Bioinformatics	Transcription Factor Co-Occurrence using Market Basket analysis
tf-comb	1.0.3	tf-comb/py39/1.0	None	application	Bioinformatics	Transcription Factor Co-Occurrence using Market Basket analysis
tf-comb	1.0.3	tf-comb/py310/1.0	None	application	Bioinformatics	Transcription Factor Co-Occurrence using Market Basket analysis
tf-comb	1.1	tf-comb/py38/1.1	None	application	Bioinformatics	Transcription Factor Co-Occurrence using Market Basket analysis
tf-comb	1.1	tf-comb/py39/1.1	None	application	Bioinformatics	Transcription Factor Co-Occurrence using Market Basket analysis
tf-comb	1.1	tf-comb/py310/1.1	None	application	Bioinformatics	Transcription Factor Co-Occurrence using Market Basket analysis
theano	0.9.0	theano/py27/0.9	None	application	mathematics	Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
theano	0.9.0	theano/py35/0.9	None	application	mathematics	Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
theano	0.9.0	theano/py36/0.9	None	application	mathematics	Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
theano	1.0.3	theano/py27/1.0	None	application	mathematics	Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
theano	1.0.3	theano/py35/1.0	None	application	mathematics	Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
theano	1.0.3	theano/py36/1.0	None	application	mathematics	Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
tmhmm	2.0c	tmhmm/2.0c	None None	application	computational biology	TMHMM 2.0 predicts transmembrane helices in proteins.
tobias	0.13.3	tobias/py37/0.13	None	application	computational biology	Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
topas-mc	3.9	topas-mc/3.9	None	application	Physics	TOPAS: Tool for Particle Simulation
tophat	2.0.14	tophat/2.0	None	application	computational biology	TopHat2 is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
tophat	2.1.1	tophat/2.1	None	application	computational biology	TopHat2 is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
tpmcalculator	0.0.4	tpmcalculator/0.0.4	None	application	bioinformatics	TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files.
transcriptm	0.2	transcriptm/0.2	None	application	bioinformatics	Metagenomics analyses.
transdecoder	2.0.1	transdecoder/2.0	None	application	computational biology	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	3.0.1	transdecoder/3.0	None	application	computational biology	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.
transformers	4.31.0	transformers/py39/4.31	None	application	machine learning	State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch
transformers	4.31.0	transformers/py310/4.31	None	application	machine learning	State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch
transformers	4.46.3	transformers/py310/4.46	None	application	machine learning	State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch
transformers	4.46.3	transformers/py311/4.46	None	application	machine learning	State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch
transformers-gpu	4.31.0	transformers-gpu/py39/4.31	None	application	machine learning	State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch
transformers-gpu	4.31.0	transformers-gpu/py310/4.31	None	application	machine learning	State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch
transformers-gpu	4.46.3	transformers-gpu/py310/4.46	None	application	machine learning	State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch
transformers-gpu	4.46.3	transformers-gpu/py311/4.46	None	application	machine learning	State-of-the-art Natural Language Processing for TensorFlow 2.0 and PyTorch
transrate	0.1	transrate/0.1	None	application	life sciences	transrate - Quality assessment and comparison of transcriptome assemblies
treemix	1.12	treemix/1.12	None	application	computational biology	TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.
treemix	1.13	treemix/1.13	None	application	computational biology	TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.
trf	4.07b	trf/4.0	None	application	computational biology	Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
triform2	0.0.5	triform2/0.0.5	None	application	computational biology	Improved sensitivity, specificity and control of false discovery rates in ChIP-Seq peak finding.
trim_galore	0.4.5	trim_galore/0.4	None	application	computational biology	Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control
trim_galore	0.6.5	trim_galore/0.6	None	application	computational biology	Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control
trimmomatic	0.33	trimmomatic/0.33	None	application	computational biology	A flexible read trimming tool for Illumina NGS data
trimmomatic	0.36	trimmomatic/0.36	None	application	computational biology	A flexible read trimming tool for Illumina NGS data
trimmomatic	0.38	trimmomatic/0.38	None	application	computational biology	A flexible read trimming tool for Illumina NGS data
trimmomatic	0.39	trimmomatic/0.39	None	application	computational biology	A flexible read trimming tool for Illumina NGS data
trinity	2.11.0	trinity/2.11	None	application	computational biology	Trinity RNA-Seq de novo transcriptome assembly
trinity	2.12.0	trinity/2.12	None	application	computational biology	Trinity RNA-Seq de novo transcriptome assembly
trinity	2.13.2	trinity/2.13	None	application	computational biology	Trinity RNA-Seq de novo transcriptome assembly
trinity	2.15.1	trinity/2.15	None	application	computational biology	Trinity RNA-Seq de novo transcriptome assembly
trinity	2.4.0	trinity/2.4	None	application	computational biology	Trinity RNA-Seq de novo transcriptome assembly
trinity	2.6.6	trinity/2.6	None	application	computational biology	Trinity RNA-Seq de novo transcriptome assembly
trinity	2.8.4	trinity/2.8	None	application	computational biology	Trinity RNA-Seq de novo transcriptome assembly
trinity	2.9.1	trinity/2.9	None	application	computational biology	Trinity RNA-Seq de novo transcriptome assembly
trinity	r2013-11-10	trinity/r2013-11-10	None	application	computational biology	Trinity RNA-Seq de novo transcriptome assembly
trinity	r2014-04-13p1	trinity/r2014-04-13p1	None	application	computational biology	Trinity RNA-Seq de novo transcriptome assembly
trinotate	2.0.2	trinotate/2.0	None	application	computational biology	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.
trinotate	3.2.1	trinotate/3.2	None	application	computational biology	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.
trinotate	r2013-11-10	trinotate/r2013-11-10	None	application	computational biology	Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.
trycycler	0.5.5	trycycler/0.5	None	application	bioinformatics	A tool for generating consensus long-read assemblies for bacterial genomes
twincons	0.6.2.dev0	twincons/0.6	None	application	Biology	This projects provides several packages for analysis of MSAs comprised of two sequence groups.
twobittofa	1.0	twobittofa/1.0	None	unknown	unknown	This is a bioinformatics, freely downloadable command-line software (linux.x86_64) provided by the UCSC
ucsc-bedgraphtobigwig	455	ucsc-bedgraphtobigwig/455	None	application	computational biology	Convert a bedGraph file to bigWig format.
ucsc-bigwigaverageoverbed	377	ucsc-bigwigaverageoverbed/377	None	application	computational biology	Compute average score of big wig over each bed, which may have introns.
ucsc-fatotwobit	377	ucsc-fatotwobit/377	None	application	computational biology	Convert DNA from fasta to 2bit format
ucsc-liftover	366	ucsc-liftover/366	None	application	computational biology	The Batch Coordinate Conversion (liftOver) utility converts genome coordinates and genome annotation files between assemblies.
ucsc-twobittofa	357	ucsc-twobittofa/357	None	application	computational biology	Convert all or part of .2bit file to fasta
ucsc-twobittofa	377	ucsc-twobittofa/377	None	application	computational biology	Convert all or part of .2bit file to fasta
udunits2	2.2.26	udunits2/2.2	compiler/pgi/20 compiler/intel/20	library	runtime support
ufcg	1.0.6	ufcg/1.0	None	application	computational biology	UFCG pipeline provides methods for a genome-wide taxonomic profiling and annotation of your own biological sequences of Fungi.
uiowa_bd	2023.06.28	uiowa_bd/2023.06.28	compiler/intel/20:openmpi/4.1	application	Brownian Dynamics	uiowa_bd is a parallelized program that performs Brownian dynamics (BD) simulations of macromolecules.
ultraplex	1.2.9	ultraplex/1.2	None	application	computational biology	fastq demultiplexer
umap-learn	0.2.4	umap-learn/py36/0.2	None	application	learning algorithm	Uniform Manifold Approximation and Projection
umap-learn	0.3.10	umap-learn/py37/0.3	None	application	learning algorithm	Uniform Manifold Approximation and Projection
umi_tools	1.0.1	umi_tools/1.0	None	application	Bioinformatics	Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs)
unicycler	0.4.8	unicycler/0.4	None	application	bioinformatics	Hybrid assembly pipeline for bacterial genomes
unicycler	0.5.0	unicycler/0.5	None	application	bioinformatics	Hybrid assembly pipeline for bacterial genomes
unikmer	0.18.7	unikmer/0.18	None	application	Biology	unikmer: toolkit for nucleic acid k-mer analysis, including set operations on k-mers (sketch) optional with TaxIDs but without count information.
uropa	4.0.2	uropa/4.0	None	application	Biology	UROPA (Universal RObust Peak Annotator) is a command line based tool, intended for genomic region annotation from e.g. peak calling. It detects the most appropriate annotation by taking parameters such as feature type, anchor, direction and strand into account. Furthermore, it allows filtering for GTF attribute values, e.g. protein_coding.
usearch	10.0.240	usearch/10.0	None	application	computational biology	USEARCH is a unique sequence analysis tool with thousands of users world-wide.
usearch	11.0.667	usearch/11.0	None	application	computational biology	USEARCH is a unique sequence analysis tool with thousands of users world-wide.
usearch	5.2	usearch/5.2	None	application	computational biology	USEARCH is a unique sequence analysis tool with thousands of users world-wide.
usearch	6.1	usearch/6.1	None	application	computational biology	USEARCH is a unique sequence analysis tool with thousands of users world-wide.
usearch	7.0	usearch/7.0	None	application	computational biology	USEARCH is a unique sequence analysis tool with thousands of users world-wide.
varscan	2.3	varscan/2.3	None	application	computational biology	Variant calling and somatic mutation/CNV detection for next-generation sequencing data
varscan	2.4.4	varscan/2.4	None	application	computational biology	Variant calling and somatic mutation/CNV detection for next-generation sequencing data
vasp	5.4.4	vasp/5.4r2scan	compiler/intel/20:openmpi/4.1	library	runtime support
vasp	5.4.4	vasp/5.4solpp	compiler/intel/20:openmpi/4.1	library	runtime support
vasp	5.4.4	vasp/5.4	compiler/intel/20:openmpi/4.1	library	runtime support
vasp	6.2.1	vasp/6.2	compiler/intel/19:openmpi/4.1	library	runtime support
vasp	6.2.1vtst	vasp/6.2vtst	compiler/intel/19:openmpi/4.1	library	runtime support
vasp	6.3.1	vasp/6.3sol	compiler/intel/20:openmpi/4.1	library	runtime support
vasp	6.3.1	vasp/6.3vtst	compiler/intel/20:openmpi/4.1	library	runtime support
vasp	6.3.1	vasp/6.3	compiler/intel/20:openmpi/4.1	library	runtime support
vasp	6.4.1	vasp/6.4sol	compiler/intel/20:openmpi/4.1	library	runtime support
vasp	6.4.1	vasp/6.4vtst	compiler/intel/20:openmpi/4.1	library	runtime support
vasp	6.4.3	vasp/6.4	compiler/intel/20:openmpi/4.1	library	runtime support
vasp	6.5.1	vasp/6.5	compiler/intel/20:openmpi/4.1	library	runtime support
vasp-acc	6.2.1	vasp-acc/6.2	compiler/intel/19	library	runtime support
vasp-acc	6.3.1	vasp-acc/6.3	compiler/intel/19 compiler/nvhpc/21.9:openmpi/3.1	library	runtime support
vasp-acc	6.4.1	vasp-acc/6.4	compiler/nvhpc/21.9:openmpi/3.1	library	runtime support
vasp-acc	6.4.3	vasp-acc/6.4	compiler/nvhpc/24.5:openmpi/4.1	library	runtime support
vasp-acc	6.5.1	vasp-acc/6.5ml	compiler/nvhpc/24.5:openmpi/4.1	library	runtime support
vasp-acc	6.5.1	vasp-acc/6.5	compiler/nvhpc/24.5:openmpi/4.1	library	runtime support
vaspkit	1.5.1	vaspkit/1.5	None	application	Chemistry	Perform high throughput analysis from data generated by VASP.
vcf-kit	0.1.6	vcf-kit/0.1	None	application	Utilities	Assorted utilities for the variant call format
vcf2maf	1.6.18	vcf2maf/1.6	None	application	computational biology	Convert a VCF into a MAF where each variant is annotated to only one of all possible gene isoforms
vcflib	1.0.2	vcflib/1.0	None	application	Utilities	Command-line tools for manipulating VCF files
vcfsort	0.1	vcfsort/0.1	None	application	computational biology	Sorts a VCF file (for human) by chromosome.
vcfstats	0.6.0	vcfstats/py39/0.6.0	None	application	statistics	Powerful statistics for VCF files
vcfstats	0.6.0	vcfstats/py310/0.6.0	None	application	statistics	Powerful statistics for VCF files
vcftools	0.1.16	vcftools/0.1	None	application	computational biology	A set of tools written in Perl and C++ for working with VCF files.
vcontact2	0.9.19	vcontact2/0.9	None	application	Virology	Viral Contig Automatic Clustering and Taxonomy
velvet	1.2.10	velvet/1.2	None	application	computational biology	Velvet - Sequence assembler for very short reads
velvetoptimiser	2.2.6	velvetoptimiser/2.2	None	application	computational biology	Automatically optimise three of Velvet's assembly parameters.
verifybamid2	2.0.1	verifybamid2/2.0	None	application	DNA sequencing	A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
verkko	2.0	verkko/2.0	None	application	computational biology	Assembler for hybrid combinations of long reads
vesta	3.5.8	vesta/3.5	None	application	visualization	VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies.
vflp	2020.04.19	vflp/2020.04.19	None	application	computational chemistry	VFLP is VirtualFlow for Ligand Preparation
vftools	0.0.2020.05.17	vftools/2020.05.17	None	application	computational chemistry	VFTools is a a loose collection of additional tools and scripts which can be useful when using VirtualFlow.
vfvs	2020.04.23	vfvs/2020.04.23	None	application	computational chemistry	VFVS is VirtualFlow for Ligand Screenings
vfvs	2022.07.21	vfvs/2022.07.21	None	application	computational chemistry	VFVS is VirtualFlow for Ligand Screenings
vg	1.63.1	vg/1.63	None	application	genomics	Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods
vgas	0.0.2020.07.22	vgas/2020.07.22	None	application	genomics	VGAS (viral genome annotation system) is a system combing ab initio method and similarity-based method, which can perform the functions of virus gene finding and function annotating merely depending on the gene sequence itself.
vibrant	1.0.1	vibrant/1.0	None	application	computational biology	Virus Identification By iteRative ANnoTation
vibrant	1.2.1	vibrant/1.2	None	application	computational biology	Virus Identification By iteRative ANnoTation
viennarna	2.3.3	viennarna/2.3	None	application	computational biology	The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
vigor4	0.0.2020.07.02	vigor4/2020.07.02	None	application	bioinformatics	VIGOR4 (Viral Genome ORF Reader) is a Java application to predict protein sequences encoded in viral genomes.
vim	8.1.0960	vim/8.1	None	application	Utility	Vim is a greatly improved version of the good old UNIX editor Vi
viral_consensus	0.0.5	viral_consensus/0.0.5	None	application	bioinformatics	Fast viral consensus genome reconstruction
virema	0.6	virema/0.6	None	application	computational biology	ViReMa (Viral Recombination Mapper) detects and reports recombination or fusion events in virus genomes using deep sequencing datasets.
virhostmatcher	1.0.0	virhostmatcher/1.0	None	application	computational biology	VirHostMatcher, matching hosts of viruses based on oligonucleotide frequency (ONF) comparison.
virhostmatcher-net	0.0.2021.08.29	virhostmatcher-net/2021.08.29	None	application	computational biology	VirHostMatcher-Net: A network-based computational tool for predicting virus-host interactions.
virsorter	1.0.6	virsorter/1.0	None	application	unknown	VirSorter2 -- A multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes
virsorter	2.1	virsorter/2.1	None	application	unknown	VirSorter2 -- A multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes
visit	2.10.2	visit/2.10	None	application	utility	VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.
vistasoft	0fa6c4a	vistasoft/0fa6c4a	None	application	matlab toolbox	VISTASOFT contains Matlab code to perform a variety of analysis on MRI data, including functional MRI and diffusion MRI.
vmd	1.9.3	vmd/1.9	None	application	molecular dynamics	VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.
vrhyme	1.1.0	vrhyme/1.1	None	application	bioinformatics	vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs).
vs-code	1.90.2	vs-code/1.90	None	application	Development	Visual Studio Code
vs-code-cli	1.90.2	vs-code-cli/1.90	None	application	Development	Visual Studio Code
vsearch	2.10.0	vsearch/2.10	None	application	computational biology	A versatile open source tool for metagenomics (USEARCH alternative)
vsearch	2.18.0	vsearch/2.18	None	application	computational biology	A versatile open source tool for metagenomics (USEARCH alternative)
wannier90	3.1	wannier90/3.1	compiler/gcc/10:openmpi/4.0 compiler/intel/20:openmpi/4.0 compiler/intel/19:openmpi/4.0 compiler/intel/19:openmpi/4.1 compiler/gcc/11:openmpi/4.1 compiler/gcc/10:openmpi/4.1 compiler/gcc/9:openmpi/4.0 compiler/intel/2024:openmpi/4.1 compiler/intel/20:openmpi/4.1	library	runtime support
wannierberri	0.11.1	wannierberri/py38/0.11	None	application	physics	Advanced tool for Wannier interpolation and integration of k-space integrals
wannierberri	0.11.1	wannierberri/py39/0.11	None	application	physics	Advanced tool for Wannier interpolation and integration of k-space integrals
wanniertools	2.7.0	wanniertools/2.7	compiler/intel/20:openmpi/4.1	application	chemistry
weblogo	3.7.4	weblogo/3.7	None	application	Utility	WebLogo3 : Sequence Logos Redrawn
wevote	1.8	wevote/1.8	None	library	runtime support
wgddetector	1.1	wgddetector/1.1	None	application	Biology	WGDdetector: a pipeline for whole genome duplication (WGD) detecting with the genome or transcriptome annotations.
wgrib	1.8	wgrib/1.8	compiler/intel/20 compiler/pgi/20	application	file processing	WGRIB is a program to manipulate, inventory and decode GRIB files.
wgrib2	2.0.8	wgrib2/2.0	None	application	utility	Utility to read and write grib2 files
wgrib2	3.1.3	wgrib2/3.1	None	application	utility	Utility to read and write grib2 files
wtdbg	2.5	wtdbg/2.5	None	application	Bioinformatics	Wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
xcrysden	1.5.60	xcrysden/1.5	None	application	physics	XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.
xcrysden	1.6.2	xcrysden/1.6	None	application	physics	XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.
xpclr	1.1.2	xpclr/1.1	None	application	Bioinformatics	Code to compute xp-clr values to detect selection as per Chen, Patterson & Reich 2010.
xzutils	5.2	xzutils/5.2	compiler/intel/18 compiler/intel/19 compiler/gcc/10 compiler/gcc/9 None compiler/intel/20 compiler/pgi/20 compiler/gcc/11	library	runtime support
yambo	5.2.3	yambo/5.2	compiler/gcc/11:openmpi/4.1	application	realistic materials	Open-source many-body perturbation theory and time-dependent density functional theory
yaml-cpp	0.7	yaml-cpp/0.7	compiler/gcc/10 compiler/intel/20	library	runtime support
zerone	1.0	zerone/1.0	None	application	computational biology	Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. After the job is done, Zerone checks the results and tells you whether it passes the quality control.
zlib	1.2	zlib/1.2	compiler/intel/2021 compiler/gcc/11 compiler/intel/18 compiler/gcc/10 compiler/pgi/20 None compiler/intel/20 compiler/intel/19 compiler/gcc/9	library	runtime support
zorro	2011.12.01	zorro/2011.12.01	None	application	bioinformatics	ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple sequence alignment.

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