Available Software for Crane

HCC provides some software packages via the Singularity container software. If you do not see a desired package in the module list below, please check the Using Singularity 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 2019-05-23T23:19:37CDT

Name Version Module Name Prerequisites Type Domain Description
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 0.3 CNVnator/0.3 compiler/gcc/4.9 application genotyping CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
GSL 1.16 GSL/1.16 compiler/gcc/4.9 compiler/intel/13 library runtime support
HTSlib 1.2 HTSlib/1.2 compiler/gcc/4.8 application computational biology HTSlib - the core library used by samtools and bcftools.
LIS 7.0r LIS/7.0r compiler/intel/13:openmpi/1.8 library runtime support
LIS 7.2r LIS/7.2r compiler/intel/13:openmpi/1.8 library runtime support
MEME 4.11.3 MEME/4.11 None 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/.
MET 5.0 MET/5.0 None library runtime support
NCL 6.0 NCL/6.0 compiler/intel/13 application utility A library of graphics utilites from the Natl. Center for Atmospheric Research.
NCL 6.1 NCL/6.1 None application utility A library of graphics utilites from the Natl. Center for Atmospheric Research.
NCL 6.3 NCL/6.3 None application utility A library of graphics utilites from the Natl. Center for Atmospheric Research.
NCL 6.4 NCL/6.4 None application utility A library of graphics utilites from the Natl. Center for Atmospheric Research.
NCO 4.3 NCO/4.3 compiler/gcc/4.7 compiler/gcc/4.8 compiler/pgi/13 compiler/pgi/12 compiler/intel/12 compiler/intel/13 library runtime support
NCO 4.4 NCO/4.4 compiler/intel/12 compiler/gcc/4.7 compiler/pgi/13 compiler/intel/13 compiler/pgi/12 compiler/gcc/4.8 library runtime support
NCO 4.4.6 NCO/4.4 compiler/pgi/15 compiler/intel/16 compiler/intel/15 library runtime support
NCO 4.5.5 NCO/4.5 compiler/intel/15 library runtime support
NCO 4.6.6 NCO/4.6 compiler/intel/15 compiler/pgi/15 compiler/pgi/13 compiler/pgi/14 compiler/pgi/12 library runtime support
NUWRF NUWRF NUWRF/intel None library runtime support
PNG 1.2.50 PNG/1.2 compiler/intel/13 library runtime support
R 3.0 R/3.0 compiler/intel/13 None compiler/intel/12 application mathematics Microsoft R Open is the enhanced distribution of R from Microsoft Corporation.
R 3.1 R/3.1 None application mathematics Microsoft R Open is the enhanced distribution of R from Microsoft Corporation.
R 3.2 R/3.2 None compiler/intel/15 application mathematics Microsoft R Open is the enhanced distribution of R from Microsoft Corporation.
R 3.3 R/3.3 None application mathematics Microsoft R Open is the enhanced distribution of R from Microsoft Corporation.
R 3.4.4 R/3.4 None application mathematics Microsoft R Open is the enhanced distribution of R from Microsoft Corporation.
R 3.5.1 R/3.5 None application mathematics Microsoft R Open is the enhanced distribution of R from Microsoft Corporation.
RAPSearch2 2.19 RAPSearch2/2.19 None application computational biology RAPSearch2 is a tool for fast protein similarity searches.
SRAtoolkit 2.8 SRAtoolkit/2.8 None application computational biology The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
SRAtoolkit 2.9 SRAtoolkit/2.9 None application computational biology The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
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.
TrimGalore 0.4.5 TrimGalore/0.4 None library runtime support
WRF WRF WRF/1.0 compiler/intel/16:openmpi/1.10 compiler/intel/15:openmpi/1.10 compiler/pgi/15:openmpi/1.10 library runtime support
WRF WRF WRF/1.1 compiler/pgi/15:openmpi/1.10 library runtime support
WRF WRF WRF/pgi None library runtime support
WRF WRF WRF/WRF None library runtime support
WRF WRF WRF/intel None 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.
abacus 1.0.1 abacus/1.0 compiler/intel/13:openmpi/1.8 library runtime support
abaqus 2019 abaqus/2019 None application Engineering Abaqus is a software suite for finite element analysis and computer-aided engineering.
abaqus 6.14.2 abaqus/6.14.2 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 8.0.8 abinit/8.0 compiler/intel/12:openmpi/1.8 application computational chemistry ABINIT is a package whose main program allows one to find the total energy.
abinit 8.4.2 abinit/8.4 compiler/intel/15:openmpi/1.10 application computational chemistry ABINIT is a package whose main program allows one to find the total energy.
abricate 0.8.13 abricate/0.8 None application Biology Mass screening of contigs for antibiotic resistance genes
abyss 2.1.0 abyss/2.1 compiler/gcc/6.1:openmpi/2.1 application bioinformatics ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes.
afni 18.2.06 afni/18.2 None application MRI AFNI is a suite of programs for looking at and analyzing 3D brain images.
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.
agfusion 1.0 agfusion/1.0 None application Biology AGFusion is a python package for annotating gene fusions from the human or mouse genomes.
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 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
allpathslg Latest allpathslg/latest compiler/gcc/4.7 application biology
anaconda 2.7 anaconda/2.7 None application system
anaconda 3.3 anaconda/3.3 None application system
anaconda 3.4 anaconda/3.4 None application system
anaconda 4.3 anaconda/4.3 None application system
anaconda 4.6 anaconda/4.6 None application system
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.
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
apkid 1.0.0 apkid/1.0 None application Malware APKiD is Android Application Identifier for Packers, Protectors, Obfuscators and Oddities - PEiD for Android.
aria2 1.23.0 aria2/1.23 None application tool aria2 is a lightweight multi-protocol & multi-source command-line download utility.
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.
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.
asreml 3.0 asreml/3.0 None application data analysis ASReml
asreml 4.1 asreml/4.1 None application data analysis ASReml
atk 13.8.2 atk/13.8.2 compiler/gcc/4.7:mpich2/1.5 application Chemistry
atk 2014.1 atk/2014.1 compiler/gcc/4.7:mpich2/1.5 application Chemistry
atk 2015.1 atk/2015.1 compiler/gcc/4.7:mpich2/1.5 application Chemistry
atk 2016.3 atk/2016.3 compiler/gcc/4.7:mpich2/1.5 application Chemistry
augustus 3.0 augustus/3.0 None compiler/gcc/4.9 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.
autoconf 2.69 autoconf/2.69 None application Utilities Extensible M4 macros that produce shell scripts to configure software source code packages.
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.
automake 1.14 automake/1.14 None application Utilities Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards.
automake 1.15 automake/1.15 None application Utilities Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards.
awscli 1.1.120 awscli/1.11 None application utility The AWS CLI is an open source tool built on top of the AWS SDK for Python (Boto) that provides commands for interacting with AWS services.
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.
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.
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
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.
bcftools 1.1 bcftools/1.1 compiler/gcc/4.8 application computational biology BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
bcftools 1.2 bcftools/1.2 compiler/gcc/4.8 application computational biology BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
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. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
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. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
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. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
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
bcl2fastq 2.17 bcl2fastq/2.17 compiler/gcc/4.7 application biology bcl2fastq can be used to demultiplex data and convert BCL files to FASTQ file formats for downstream analysis
beagle 4.1_21Jan17 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.
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.
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
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.
binutils 2.30 binutils/2.30 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
bioconductor 3.4 bioconductor/3.4 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-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 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 1.7.2 bioperl/1.7 None application computational biology BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.
biopieces 1.0 biopieces/1.0 compiler/gcc/4.8:openmpi/1.6 application computational biology The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks.
biopython 1.70 biopython/py27/1.70 None application biological computation Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
biopython 1.70 biopython/py35/1.70 None application biological computation Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
biopython 1.70 biopython/py36/1.70 None application biological computation Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
biopython 1.71 biopython/py27/1.71 None application biological computation Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
biopython 1.71 biopython/py36/1.71 None application biological computation Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
biopython 1.71 biopython/py35/1.71 None application biological computation Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
biosamtools 1.38 biosamtools/1.38 None application computational biology
bismark 0.14.2 bismark/0.14 None application computational biology Bisulfite read mapper and methylation caller.
bismark 0.19.0 bismark/0.19 None application computational biology Bisulfite read mapper and methylation caller.
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 modulerc blast/modulerc 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 34 blat/34 None application computational biology Blat is an alignment tool like BLAST, but it is structured differently. On DNA, Blat works by keeping an index of an entire genome in memory. Thus, the target database of BLAT is not a set of GenBank sequences, but instead an index derived from the assembly of the entire genome.
blat 35x1 blat/35x1 None application computational biology Blat is an alignment tool like BLAST, but it is structured differently. On DNA, Blat works by keeping an index of an entire genome in memory. Thus, the target database of BLAT is not a set of GenBank sequences, but instead an index derived from the assembly of the entire genome.
boost 1.44 boost/1.44 None compiler/gcc/4.9 application System Environment/Base Boost provides free peer-reviewed portable C++ source libraries.
boost 1.54 boost/1.54 compiler/gcc/4.9 application System Environment/Base Boost provides free peer-reviewed portable C++ source libraries.
boost 1.55 boost/1.55 compiler/gcc/4.9:openmpi/1.10 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 1.57 boost/1.57 compiler/gcc/4.9 application System Environment/Base Boost provides free peer-reviewed portable C++ source libraries.
boost 1.59 boost/1.59 compiler/gcc/6.1 compiler/gcc/5.4 compiler/intel/13 compiler/gcc/4.9 application System Environment/Base Boost provides free peer-reviewed portable C++ source libraries.
boost 1.63 boost/1.63 compiler/intel/16 compiler/gcc/6.1 application System Environment/Base Boost provides free peer-reviewed portable C++ source libraries.
boost 1.64 boost/1.64 compiler/gcc/7.1 application System Environment/Base Boost provides free peer-reviewed portable C++ source libraries.
boost 1.66 boost/1.66 compiler/gcc/7.1 compiler/gcc/8.2 application System Environment/Base Boost provides free peer-reviewed portable C++ source libraries.
boost 1.69 boost/1.69 compiler/gcc/8.2 application System Environment/Base Boost provides free peer-reviewed portable C++ source libraries.
bowtie 1.0 bowtie/1.0 None application computational biology Ultrafast, memory-efficient short read aligner
bowtie 1.1.2 bowtie/1.1 None application computational biology Ultrafast, memory-efficient short read aligner
bowtie 2.2.6 bowtie/2.2 None application computational biology Ultrafast, memory-efficient short read aligner
bowtie 2.3.4 bowtie/2.3 None application computational biology Ultrafast, memory-efficient short read aligner
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.
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/py27 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/py35 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/py36 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.
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.
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
bx-python 0.8.1 bx-python/py27/0.8 None application computational biology Tools for manipulating biological data, particularly multiple sequence alignments
bzip2 1.0 bzip2/1.0 None 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.
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).
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.
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
cd-hit 4.6 cd-hit/4.6 None application computational biology cd-hit is a very widely used program for clustering and comparing protein or nucleotide sequences.
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 1.6 cdo/1.6 compiler/pgi/13 library runtime support
cdo 1.7.1 cdo/1.7 compiler/pgi/14 compiler/intel/15 compiler/pgi/15 library runtime support
cdo 1.8 cdo/1.8 compiler/pgi/13 library runtime support
cdo 1.8.1 cdo/1.8 compiler/pgi/15 compiler/intel/15 compiler/pgi/14 compiler/intel/16 library runtime support
cexor 1.10 cexor/1.10 None application computational biology An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates.
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 3.5.0 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
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.
compiler/gcc 4.7 compiler/gcc/4.7 None application compiler
compiler/gcc 4.8 compiler/gcc/4.8 None application compiler
compiler/gcc 4.9 compiler/gcc/4.9 None application compiler
compiler/gcc 5.4 compiler/gcc/5.4 None application compiler
compiler/gcc 6.1 compiler/gcc/6.1 None application compiler
compiler/gcc 7.1 compiler/gcc/7.1 None application compiler
compiler/gcc 8.2 compiler/gcc/8.2 None application compiler
compiler/intel 12 compiler/intel/12 None application compiler
compiler/intel 13 compiler/intel/13 None application compiler
compiler/intel 15 compiler/intel/15 None application compiler
compiler/intel 16 compiler/intel/16 None application compiler
compiler/intel 18 compiler/intel/18 None application compiler
compiler/intel 19 compiler/intel/19 None application compiler
compiler/pgi 12 compiler/pgi/12 None application compiler
compiler/pgi 13 compiler/pgi/13 None application compiler
compiler/pgi 14 compiler/pgi/14 None application compiler
compiler/pgi 15 compiler/pgi/15 None application compiler
compiler/pgi 16 compiler/pgi/16 None application compiler
compiler/pgi 18 compiler/pgi/18 None application compiler
comsol 5.4 comsol/5.4 None application simulation COMSOL Multiphysics
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 1.3.1 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
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.
cp2k 2.6 cp2k/2.6 compiler/gcc/4.7:openmpi/1.8 library runtime support
cp2k 3.0 cp2k/3.0 compiler/gcc/4.7:openmpi/1.8 library runtime support
cp2k 4.1 cp2k/4.1 compiler/gcc/4.7:openmpi/1.8 library runtime support
cp2k 5.1 cp2k/5.1 compiler/gcc/4.7:openmpi/1.8 library runtime support
cp2k 6.1 cp2k/6.1 compiler/intel/16:openmpi/2.0 compiler/intel/16:openmpi/3.1 library runtime support
crest 1.0 crest/1.0 None application computational biology
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 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 cufflinks - Transcript assembly, differential expression, and differential regulation for RNA-Seq
cufflinks 2.2 cufflinks/2.2 None application computational biology cufflinks - Transcript assembly, differential expression, and differential regulation for RNA-Seq
curl 7.50 curl/7.50 None 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.
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.
deap 1.0 deap/1.0 None application computer science DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas.
deeptools 2.5.4 deeptools/2.5 None application computational biology
defiant 2019.03.02 defiant/2019.03.02 None application computational biology Differential methylation, Easy, Fast, Identification and ANnoTation.
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.
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
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.
eigen 3.3.3 eigen/3.3 None application C++ C++ template library for linear algebra
elk 4.3.6 elk/4.3 compiler/intel/13:openmpi/1.8 library runtime support
emacs 24.5 emacs/24.5 None unknown unknown
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.
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.
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. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
epoch 4.15 epoch/4.15 compiler/intel/16:openmpi/2.1 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 5.2.0rp3 esmf/5.2 compiler/intel/13 library runtime support
espresso 5.0 espresso/5.0 compiler/intel/13:openmpi/1.8 library runtime support
espresso 6.2.1 espresso/6.2 compiler/intel/15:openmpi/2.0 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.
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 exonerate/2.2 None application computational biology Exonerate - a generic tool for sequence alignment.
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
fastqc 0.10 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
faststructure 1.0 faststructure/1.0 None application computational biology A variational framework for inferring population structure from SNP genotype data.
fasttree 2.1.10 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.
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
fftw2 2.1 fftw2/2.1 compiler/intel/13 compiler/gcc/4.8 library runtime support
fftw3 3.3 fftw3/3.3 compiler/intel/13 compiler/intel/12 compiler/gcc/4.8 compiler/intel/15 compiler/gcc/4.8:openmpi/1.8 compiler/gcc/4.9 compiler/intel/12:openmpi/1.8 compiler/intel/13:openmpi/1.8 compiler/gcc/6.1:openmpi/2.0 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
flash 1.2.11 flash/1.2 compiler/gcc/4.9 application computational biology FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.
fqtrim 0.9.7 fqtrim/0.9 None application computational biology fqtrim: trimming & filtering of NGS reads.
freebayes 1.2.0 freebayes/1.2 None application Biology Bayesian haplotype-based polymorphism discovery and genotyping
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 6.0.0 freesurfer/6.0 None application computational neuroimaging An open source software suite for processing and analyzing (human) brain MRI images.
gamess 20141205R1 gamess/20141205R1 compiler/intel/13:openmpi/1.8 library runtime support
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.
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.
gaussian 09 RevD gaussian/09/RevD None application Chemistry
gaussian 09 RevE gaussian/09/RevE None application Chemistry
gaussian 16 RevE gaussian/16/RevA 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
gctb 1.0 gctb/1.0 compiler/gcc/4.9:openmpi/1.10 library runtime support
gdal 1.11 gdal/1.11 compiler/gcc/4.9 library runtime support
gdcclient 1.2.0 gdcclient/1.2 compiler/gcc/4.9 application genomics GDC provides a standard client-based mechanism in support of high performance data downloads and submission.
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.
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.
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
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.
geoparse 1.0.5 geoparse/1.0 None application Bioinformatics Python library to access Gene Expression Omnibus Database (GEO)
geos 3.5 geos/3.5 compiler/gcc/4.9 library runtime support
gffcompare 0.10.6 gffcompare/0.10 None application Annotation GffCompare by Geo Pertea
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.
git 2.17.0 git/2.17 None library tools distributed version control system
git 2.7.4 git/2.7 None library tools distributed version control system
globus-cli 1.10.1 globus-cli/1.10 None application tool Command line clients provide an interface to Globus services from the shell, and are suited for both interactive use and simple scripting use cases.
globus-cli 1.2.0 globus-cli/1.2 None application tool Command line clients provide an interface to Globus services from the shell, and are suited for both interactive use and simple scripting use cases.
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.
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.
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.
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
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 library unknown
grib-api 1.12.3 grib-api/1.12 compiler/intel/13 library runtime support
grib-api 1.14.5 grib-api/1.14 compiler/intel/15 compiler/pgi/14 compiler/pgi/15 library runtime support
gromacs 4.6 gromacs/4.6 compiler/gcc/4.8:openmpi/1.6 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 5.1.4 gromacs/5.1 compiler/gcc/4.9:openmpi/2.0 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.
gtdbtk 0.1.3 gtdbtk/0.1 None application computational biology A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
gtool 0.7.5 gtool/0.7 compiler/gcc/6.1 application computational biology GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.
gubbins 2.3.4 gubbins/2.3 None application Biology Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
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.
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.
halla 0.8.17 halla/0.8 None application computational biology HAllA: Hierarchically All-against-All Association Testing.
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.
harminv 1.4 harminv/1.4 compiler/gcc/4.9 library runtime support
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..
hdf4 4.2 hdf4/4.2 compiler/gcc/4.7 compiler/pgi/15 compiler/pgi/12 compiler/intel/13 compiler/pgi/13 compiler/gcc/4.9 compiler/gcc/4.8 compiler/intel/16 compiler/pgi/14 compiler/intel/15 compiler/intel/12 library runtime support
hdf5 1.8 hdf5/1.8 None compiler/pgi/15 compiler/pgi/13 compiler/intel/13 compiler/intel/12 compiler/gcc/4.9 compiler/gcc/4.8 compiler/pgi/12 compiler/gcc/4.7 compiler/intel/18 compiler/pgi/14 library runtime support
hdf5 1.8.15 hdf5/1.8 compiler/intel/15 compiler/intel/16 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.
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
hmmer 3.1 hmmer/3.1 compiler/gcc/4.8:openmpi/1.6 compiler/gcc/4.8:openmpi/1.8 application computational biology HMMER biosequence analysis using profile hidden Markov models
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 0.5.4p5 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
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.
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
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 unied approach to measure the reproducibility of ndings identied from replicate experiments and provide highly stable thresholds based on reproducibility.
igraph 0.7 igraph/0.7 compiler/gcc/4.9 library runtime support
ima2p 1.0 ima2p/1.0 compiler/gcc/6.1:openmpi/1.10 application Bayesian MCMC IMa2p is a parallel implementation of IMa2, using OpenMPI-C++ - a Bayesian MCMC based method for inferring population demography under the IM (Isolation with Migration) model.
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.
impute2 2.3.2 impute2/2.3 None application computational biology IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes.
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
interproscan 5.23-62.0 interproscan/5.23 compiler/gcc/4.8 application computational biology Scans a range of protein signatures against your sequences and provides protein functional analysis.
interproscan 5.24-63.0 interproscan/5.24 compiler/gcc/4.8 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.
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.
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.
jags 3.4 jags/3.4 compiler/intel/15 application mathematics JAGS is Just Another Gibbs Sampler.
jags 4.2 jags/4.2 compiler/intel/15 compiler/gcc/4.9 application mathematics JAGS is Just Another Gibbs Sampler.
jags 4.3 jags/4.3 compiler/intel/15 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.
java 1.6 java/1.6 None application system Java JDK.
java 1.7 java/1.7 None application system Java JDK.
java 1.8 java/1.8 None application system Java JDK.
jellyfish 2.2.0 jellyfish/2.2 None application computational biology Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
jellyfish 2.2.7 jellyfish/2.2 compiler/gcc/4.9 application computational biology Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
jmosaics 1.10 jmosaics/1.10 None application computational biology Joint analysis of multiple ChIP-Seq data sets.
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
justorthologs 0.0.20190308 justorthologs/0.0.20190308 None application Biology JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm.
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
kaiju 1.4 kaiju/1.4 compiler/gcc/4.9 application Bioinformatics
kaiju 1.5.0 kaiju/1.5 compiler/gcc/4.9 application Bioinformatics
kaiju 1.7.0 kaiju/1.7 compiler/gcc/4.9 application Bioinformatics
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 0.42.3 kallisto/0.42 compiler/gcc/4.8 library runtime support
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-gpu 2.2.4 keras-gpu/py36/2.2 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
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.
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.
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 10Aug2015 lammps/10Aug2015 compiler/intel/15:openmpi/1.8 library runtime support
lammps 10Feb2017 lammps/10Feb2017 compiler/gcc/6.1:openmpi/2.0 compiler/intel/15:openmpi/1.10 library runtime support
lammps 12Dec2018 lammps/12Dec2018 compiler/intel/16:openmpi/3.1 library runtime support
lammps 15MAY2015 lammps/15May15 compiler/gcc/4.9:openmpi/1.8 compiler/gcc/4.9:openmpi/2.1 library runtime support
lammps 22Aug2018 lammps/22Aug2018 compiler/intel/16:openmpi/3.1 library runtime support
lammps 30Oct2014 lammps/30Oct2014 compiler/gcc/4.8:openmpi/1.8 library runtime support
lammps 31Jan2014 lammps/31Jan2014 compiler/gcc/4.8:openmpi/1.6 library runtime support
largenet 0.6 largenet/0.6 compiler/gcc/4.9 library runtime support
last 1.0 last/1.0 compiler/gcc/4.9 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.
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).
libctl 3.2 libctl/3.2 compiler/gcc/4.9 compiler/gcc/6.1 library runtime support
libint 1.1 libint/1.1 compiler/gcc/4.7 application Computational Chemistry Libint is a software stack for computing integrals used in molecular quantum mechanics
libxc 2.2.3 libxc/2.2 compiler/intel/13 library runtime support
libxml2 2.7 libxml2/2.7 compiler/gcc/4.9 library runtime support
libxml2 2.9 libxml2/2.9 compiler/gcc/4.9 library runtime support
libxslt 1.1 libxslt/1.1 compiler/gcc/4.9 library runtime support
lmdb 0.9 lmdb/0.9 None library unknown Lightning memory-mapped database library.
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.
lsdyna 10.0 lsdyna/10.0 None unknown unknown
lsdyna 10.1 lsdyna/10.1 None unknown unknown
lsdyna 5.1.1 lsdyna/5.1.1 None unknown unknown
lsdyna 6.0.0 lsdyna/6.0.0 None unknown unknown
lsdyna 6.1.2 lsdyna/6.1.2 None unknown unknown
lsdyna 7.0.0 lsdyna/7.0.0 None unknown unknown
lsdyna 7.1.1 lsdyna/7.1.1 None unknown unknown
lsdyna 8.0.0 lsdyna/8.0.0 None unknown unknown
lsdyna 8.0.1 lsdyna/8.0.1 None unknown unknown
lsdyna 8.1.0 lsdyna/8.1.0 None unknown unknown
lsdyna 9.0.1 lsdyna/9.0.1 None unknown unknown
lsdyna 9.2.0 lsdyna/9.2.0 None unknown unknown
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 1.4 m4/1.4 None application Utilities GNU M4 is an implementation of the traditional Unix macro processor.
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.
macs2 2.1.1 macs2/2.1 None application computational biology MACS -- Model-based Analysis of ChIP-Seq
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
maker 2.31.10 maker/2.31 None application computational biology MAKER is a genome annotation pipeline for prokaryotic and smaller eukaryotic organisms.
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.
mashmap 2.0 mashmap/2.0 None application computational biology A fast approximate aligner for long DNA sequences
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.
mathematica 10.0 mathematica/10.0 None unknown unknown
mathematica 10.4 mathematica/10.4 None unknown unknown
mathematica 11.0 mathematica/11.0 None unknown unknown
mathematica 11.3 mathematica/11.3 None unknown unknown
mathematica 9.0 mathematica/9.0 None unknown unknown
matio 1.5 matio/1.5 compiler/gcc/4.9 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
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.
maxquant 1.6.6.0 maxquant/1.6 None application biochemistry MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
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
meep 1.3 meep/1.3 None library runtime support
meep_parallel 1.3 meep_parallel/1.3 compiler/gcc/4.9:openmpi/1.10 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-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.
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.
meme-suite 4.12.0 meme-suite/4.12 compiler/gcc/6.1:openmpi/2.0 application computational biology
metaphlan 1.7 metaphlan/1.7 None application computational biology 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.
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
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.
minimap2 2.16 minimap2/2.16 None application bioinformatics A versatile pairwise aligner for genomic and spliced nucleotide sequences.
misis 1.0 misis/1.0 None application computational biology
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
modeller 9.19 modeller/9.19 None unknown unknown
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.
mono 4.6 mono/4.6 None application compiler Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.
mono 5.10 mono/5.10 None application compiler Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.
moose 1.0 moose/1.0 compiler/gcc/6.1:openmpi/2.0 library runtime support
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.
mothur 1.35.1 mothur/1.35 compiler/gcc/4.9:openmpi/1.10 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 1.41.3 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.
mpb 1.5 mpb/1.5 compiler/gcc/6.1:openmpi/2.0 library runtime support
mpiblast 1.6 mpiblast/1.6 compiler/gcc/4.8:openmpi/1.6 application computational biology mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST.
mpich2 1.5 mpich2/1.5 compiler/gcc/4.7 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.
mspkmercounter 0.10.0 mspkmercounter/0.10 None application Biology MSPKmerCounter is a k-mer counter based on the minimum substring partitioning technique.
mugsy v1r2.3 mugsy/v1r2.3 None application computational biology
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/0.8 None application computational biology Aggregate results from bioinformatics analyses across many samples into a single report
multiqc 1.6 multiqc/py36/1.6 None application computational biology Aggregate results from bioinformatics analyses across many samples into a single report
multiqc 1.6 multiqc/py27/1.6 None application computational biology Aggregate results from bioinformatics analyses across many samples into a single report
multiqc 1.6 multiqc/py35/1.6 None application computational biology Aggregate results from bioinformatics analyses across many samples into a single report
multiwell 2017 multiwell/2017 compiler/gcc/6.1:openmpi/2.1 application chemistry MultiWell calculates time dependent concentrations, reaction yields, vibrational distributions, and rate constants as functions of temperature and pressure for multi-well, multi-channel unimolecular reactions systems that consist of stable species and multiple isomerization and/or dissociation reactions.
mummer 3.23 mummer/3.23 None application computational biology MUMmer - A modular system for the rapid whole genome alignment of finished or draft sequence
mummer4 4.0.0beta2 mummer4/4.0 None application Bioinformatics MUMmer is a system for rapidly aligning entire genomes
muscle 3.8 muscle/3.8 None application computational biology Popular multiple alignment software
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.
mvapich2 1.9 mvapich2/1.9 compiler/intel/13 library runtime support
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.
mytaxa 1.0 mytaxa/1.0 None application computational biology MyTaxa - Assign taxonomy to metagenomic fragments.
namd 2.12 namd/2.12 compiler/gcc/4.9:openmpi/1.10 library runtime support
ncbi-download 0.2.6 ncbi-download/0.2 None application computational biology Python scriopt for downloading bacterial and fungal genomes from NCBI.
neper 3.3.0 neper/3.3 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 4.1 netcdf/4.1 compiler/intel/13 library runtime support
netcdf 4.2 netcdf/4.2 compiler/pgi/12 compiler/intel/12 compiler/pgi/15 compiler/pgi/13 compiler/gcc/4.8 compiler/intel/13 compiler/intel/18 compiler/gcc/4.7 compiler/pgi/14 library runtime support
netcdf 4.3 netcdf/4.3 compiler/pgi/15 compiler/pgi/13 compiler/pgi/12 compiler/gcc/4.8 compiler/pgi/14 compiler/gcc/4.7 compiler/intel/13 compiler/intel/12 library runtime support
netcdf 4.4 netcdf/4.4 compiler/gcc/4.9 library runtime support
netcdf 4.4.0 netcdf/4.4 compiler/intel/15 compiler/intel/13 compiler/pgi/14 compiler/intel/18 compiler/pgi/13 compiler/intel/16 compiler/pgi/15 compiler/pgi/12 library runtime support
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.
nwchem 6.3 nwchem/6.3 compiler/intel/13:openmpi/1.6 library runtime support
nwchem 6.5 nwchem/6.5 compiler/intel/13:openmpi/1.8 library runtime support
nwchem 6.6 nwchem/6.6 compiler/intel/13:openmpi/1.8 library runtime support
oases 0.2.09 oases/0.2 compiler/gcc/6.1 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.
octopus 5.0 octopus/5.0 compiler/intel/13:openmpi/1.10 library runtime support
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.
openbugs 3.2 openbugs/3.2 None application statistics BUGS is a software package for performing Bayesian inference Using Gibbs Sampling.
opencl 1.2 opencl/1.2 None 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 If the library finds Intel's Integrated Performance Primitives on the system, it will use these proprietary optimized routines to accelerate itself.
opencv 3.1.0 opencv/3.1 None library unknown If the library finds Intel's Integrated Performance Primitives on the system, it will use these proprietary optimized routines to accelerate itself.
opencv 3.4.1 opencv/py27/3.4 None library unknown If the library finds Intel's Integrated Performance Primitives on the system, it will use these proprietary optimized routines to accelerate itself.
opencv 3.4.1 opencv/py36/3.4 None library unknown If the library finds Intel's Integrated Performance Primitives on the system, it will use these proprietary optimized routines to accelerate itself.
openmpi 1.10.2 openmpi/1.10 compiler/gcc/6.1 compiler/pgi/13 compiler/gcc/4.8 compiler/gcc/5.4 compiler/pgi/15 compiler/gcc/4.7 compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/gcc/4.9 compiler/intel/12 compiler/pgi/12 compiler/pgi/14 library runtime support
openmpi 1.6 openmpi/1.6 compiler/intel/13 compiler/gcc/4.9 compiler/pgi/12 compiler/gcc/4.8 compiler/intel/12 compiler/gcc/4.7 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 compiler/intel/15 library runtime support
openmpi 1.8 openmpi/1.8 compiler/gcc/5.4 compiler/intel/12 compiler/intel/15 compiler/intel/13 compiler/gcc/4.9 compiler/gcc/4.7 compiler/gcc/4.8 compiler/pgi/13 compiler/pgi/15 compiler/pgi/12 compiler/pgi/14 library runtime support
openmpi 2.0 openmpi/2.0 compiler/pgi/15 compiler/pgi/13 compiler/intel/16 compiler/pgi/12 compiler/intel/13 compiler/intel/12 compiler/pgi/14 compiler/intel/15 library runtime support
openmpi 2.0.1 openmpi/2.0 compiler/gcc/4.7 compiler/gcc/6.1 compiler/gcc/4.8 compiler/gcc/4.9 compiler/gcc/5.4 library runtime support
openmpi 2.1 openmpi/2.1 compiler/gcc/4.8 compiler/pgi/13 compiler/gcc/5.4 compiler/intel/12 compiler/gcc/8.2 compiler/gcc/4.7 compiler/intel/13 compiler/gcc/4.9 compiler/intel/16 compiler/intel/15 compiler/gcc/7.1 compiler/pgi/15 compiler/pgi/14 compiler/gcc/6.1 compiler/pgi/12 library runtime support
openmpi 3.1 openmpi/3.1 compiler/intel/16 library runtime support
openmx 3.7 openmx/3.7 compiler/intel/13:openmpi/1.8 library runtime support
openmx 3.8 openmx/3.8 compiler/intel/13:openmpi/1.8 library runtime support
openmx 3.8.5 openmx/3.8 compiler/intel/16:openmpi/3.1 library runtime support
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.
orthomcl 2.0.9 orthomcl/2.0 None application Biology Ortholog groups of protein sequences
p7zip 16.02 p7zip/16.02 None application compression p7zip is a port of 7za.exe for POSIX systems.
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.
pandaseq 2.9 pandaseq/2.9 compiler/gcc/4.9 application bioinformatics PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
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
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
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.
pepr 1.1.18 pepr/1.1 None application computational biology Peak-calling and Prioritization pipeline for replicated ChIP-Seq data.
peridigm 1.5 peridigm/1.5 compiler/gcc/4.9:openmpi/1.10 library runtime support
perl 5.22 perl/5.22 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.
pesmf 5.2.0rp3 pesmf/5.2 compiler/intel/13:openmpi/1.6 library runtime support
petsc 3.6 petsc/3.6 compiler/gcc/6.1:openmpi/2.0 library runtime support
petsc 3.9 petsc/3.9 compiler/gcc/6.1:openmpi/2.0 library runtime support
phdf5 1.8 phdf5/1.8 compiler/gcc/4.8:openmpi/1.6 library runtime support
phdf5 1.8.15 phdf5/1.8 compiler/pgi/12:openmpi/1.8 compiler/intel/15:openmpi/1.10 compiler/pgi/14:openmpi/1.8 compiler/pgi/15:openmpi/1.8 compiler/gcc/4.8:openmpi/1.8 compiler/gcc/4.9:openmpi/1.10 compiler/pgi/13:openmpi/1.8 compiler/gcc/4.7:openmpi/1.8 library runtime support
phobius 1.01 phobius/1.01 None application computational biology Phobius is a combined transmembrane topology and signal peptide predictor.
phonopy 1.11.12 phonopy/1.11 None library runtime support
phrap 0.990329 phrap/0.9 compiler/gcc/4.8 application computational biology Phrap is a program for assembling shotgun DNA sequence data. Cross_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat. Swat is a program for searching one or more DNA or protein query sequences, or a query profile, against a sequence database, using an efficient implementation of the Smith-Waterman or Needleman-Wunsch algorithms with linear (affine) gap penalties.
phylip 3.696 phylip/3.696 compiler/gcc/4.9 application computational biology PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees).
phylip 3.697 phylip/3.6 None application computational biology PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees).
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 PhyloPhlAn is a computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information.
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.
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 2.18.4 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 2.9.0 picard/2.9 None application computational biology A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
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.
pindel 0.2.5b9 pindel/0.2 None application computational biology
pirs 2.0.2 pirs/2.0 None application computational biology
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.
pnetcdf 4.2 pnetcdf/4.2 compiler/gcc/4.8:openmpi/1.6 library runtime support
pnetcdf 4.4 pnetcdf/4.4 compiler/gcc/4.9:openmpi/1.10 library runtime support
pomoxis 0.1.7 pomoxis/0.1 None application computational biology Pomoxis comprises APIs and command line tools for interacting and analysing Oxford Nanopore Technologies data in real time.
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.
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 2.60 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 4.9 proj/4.9 compiler/gcc/4.9 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 1.13.4 prokka/1.13 None application bioinformatics Prokka is a software tool for the rapid annotation of prokaryotic genomes.
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.
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.
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.
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.
pymeteo 0.5 pymeteo/0.5 None application geoscience General meteorological routines, skew-T/log-p plotting and working with CM1 model data.
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.
pyseer 1.2.0 pyseer/1.2 None application computational biology Sequence Elements Enrichment Analysis (SEER), python implementation
python 2.7 python/2.7 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-openstackclient 2.1.0 python-openstackclient/2.1 None application Utility OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the command set for Compute, Identity, Image, Object Store and Block Storage APIs together in a single shell with a uniform command structure.
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/py36/0.4 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.
qctool 1.4 qctool/1.4 None application computational biology QCTOOL is a command-line utility program for basic quality control of gwas datasets.
qiime 1.8 qiime/1.8 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime 1.9 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.
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.
r-asreml 4.1 r-asreml/r34/4.1 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-genometricorr 1.1.17 r-genometricorr/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/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-keras 2.2.4.1 r-keras/2.2 None application machine learning Interface to 'Keras' <https://keras.io>, a high-level neural networks 'API'.
r-markdown 0.8 r-markdown/0.8 None application R Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats.
r-regresshaplo 1.0 r-regresshaplo/1.0 None application biology This package reconstructs haplotypes from a BAM file using a penalized regression approach.
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/0.0.6 None application biology scImpute is accurate and robust imputation of single-cell RNA sequencing data.
r-seqminer 6.0 r-seqminer/6.0 None application biology SEQMINER is for sequencing variant annotation, data integration and query in R.
r-vcfr 1.5.0 r-vcfr/1.5 None application biology A package to manipulate and visualize VCF data in R.
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.
ray 2.3 ray/2.3 compiler/gcc/4.8:openmpi/1.8 compiler/gcc/4.8:openmpi/1.6 application computational biology Ray -- Parallel genome assemblies for parallel DNA sequencing.
rclone 1.44 rclone/1.44 None application Storage Rclone - rsync for cloud storage.
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 3.0.2 relion/3.0 compiler/intel/15:openmpi/1.10 library runtime support
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.
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.
revtrans 1.4 revtrans/1.4 None application computational biology RevTrans - performs a reverse translation of a peptide alignment.
rgt 0.11.4 rgt/0.11 None application computational biology Toolkit to perform regulatory genomics data analysis
rmblast 2.28 rmblast/2.28 compiler/gcc/4.8 application computational biology RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler.
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.
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
root 6.06.08 root/6.06 compiler/gcc/4.9 application big data It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage.
rosetta 3.8 rosetta/3.8 compiler/gcc/4.9:openmpi/2.0 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.
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.
ruby 2.1 ruby/2.1 None application system
saga 2.1 saga/2.1 compiler/gcc/4.9 application GIS SAGA: System for Automated Geoscientific Analyses.
saga 2.2 saga/2.2 compiler/gcc/4.9 application GIS SAGA: System for Automated Geoscientific Analyses.
saga 2.3 saga/2.3 compiler/gcc/4.9 application GIS SAGA: System for Automated Geoscientific Analyses.
sage 6.3 sage/6.3 None application mathematics 'Sage is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more.' Mission: 'Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.'
sage 8.0 sage/8.0 compiler/gcc/5.4 application mathematics 'Sage is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more.' Mission: 'Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.'
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.
samtools 0.1 samtools/0.1 None application computational biology Tools for dealing with SAM, BAM and CRAM files
samtools 1.1 samtools/1.1 compiler/gcc/4.8 application computational biology Tools for dealing with SAM, BAM and CRAM files
samtools 1.2 samtools/1.2 compiler/gcc/4.8 application computational biology Tools for dealing with SAM, BAM and CRAM files
samtools 1.3.1 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 9.3 sas/9.3 None application Applications SAS is a software suite developed by SAS Institute for advanced analytics, business intelligence, data management, and predictive analytics.
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.
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.
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/py36/1.6 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
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.
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
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.
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 settarg settarg/settarg None unknown unknown
sff2fastq 0.9 sff2fastq/0.9 None application computational biology sff2fast extracts 454 Genome Sequencer reads from a SFF file and converts them into a FASTQ formatted output
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.
shengbte 1.1.1 shengbte/1.1 compiler/gcc/4.9:openmpi/1.10 library runtime support
shortstack 3.8.5 shortstack/3.8 None application Biology ShortStack: Comprehensive annotation and quantification of small RNA genes
shovill 1.0.4 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 2.8 shtns/2.6 compiler/intel/15 application math
sickle 1.2 sickle/1.210 None application computational biology A windowed adaptive trimming tool for FASTQ files using quality
siesta 4.1.3 siesta/4.1 compiler/gcc/4.9:openmpi/1.10 compiler/intel/15:openmpi/1.10 compiler/intel/13:openmpi/1.8 library runtime support
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 computational 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.
simrna 3.20 simrna/3.20 None application computational biology SimRNA is a tool for simulations of RNA conformational dynamics
singularity 2.2 singularity/2.2 None application system Application containers enabling mobility of compute.
singularity 2.3 singularity/2.3 None application system Application containers enabling mobility of compute.
singularity 2.4 singularity/2.4 None application system Application containers enabling mobility of compute.
singularity 2.6 singularity/2.6 None application system Application containers enabling mobility of compute.
smrtlink 5.0.1 smrtlink/5.0 None application biology PacBios open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.
smrtlink 5.1.0 smrtlink/5.1 None application biology PacBios open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.
snap 2013-11-29 snap/2013-11-29 None application computational biology SNAP - (Semi-HMM-based Nucleic Acid Parser) gene prediction tool.
snippy 4.3.6 snippy/4.3 None application computational biology Rapid bacterial SNP calling and core genome alignments
snp-pipeline 0.6 snp-pipeline/0.6 None unknown unknown
snp-pipeline 0.7 snp-pipeline/0.7 None unknown unknown
snp-pipeline 1.0 snp-pipeline/1.0 None unknown unknown
snp-sites 2.3.3 snp-sites/2.3 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.
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 1.13 sonnet/py35/1.13 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.13 sonnet/py27/1.13 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.13 sonnet/py36/1.13 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.19 sonnet/py27/1.19 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.19 sonnet/py35/1.19 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.19 sonnet/py36/1.19 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.23 sonnet/py36/1.23 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.23 sonnet/py27/1.23 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.23 sonnet/py35/1.23 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.27 sonnet/py36/1.27 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.27 sonnet/py27/1.27 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
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/py36/1.19 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 1.23 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/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/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/py36/1.27 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet-gpu 1.27 sonnet-gpu/py27/1.27 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
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/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/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/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 3.8.1 spades/3.8 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spglib 1.9.9 spglib/1.9 compiler/gcc/4.9 library runtime support
spider 2.0 spider/2.0 None application computational biology Sequence-based Prediction of Local and Nonlocal Structural Features for Proteins.
spm 12 spm/12 compiler/gcc/7.1 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.
spm 8 spm/8 compiler/gcc/7.1 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
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.
stamp 2.1.3 stamp/2.1 None application Taxonomy A graphical software package for analyzing taxonomic and functional profiles.
star 2.5.3a star/2.5 compiler/gcc/4.9 application biology Spliced Transcripts Alignment to a Reference
starccm 10.01.010 starccm/10.06 None library runtime support
starccm 9.01.011 starccm/9.06 None library runtime support
stereogene 2.20 stereogene/2.20 None application sequencing StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data
strelka 2.9.10 strelka/2.9 None application computational biology Strelka calls somatic and germline small variants from mapped 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 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.
szip 2.1 szip/2.1 compiler/pgi/12 compiler/intel/12 compiler/pgi/13 compiler/intel/15 compiler/gcc/4.7 None compiler/pgi/14 compiler/gcc/4.9 compiler/intel/18 compiler/pgi/15 compiler/gcc/4.8 compiler/intel/16 compiler/intel/13 library runtime support
tabix 0.2 tabix/0.2 None application computational biology Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file
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 5.2.40 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
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 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 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 1.0.0 tensorflow/py27/1.0 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.11.0 tensorflow/py36/1.11 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.11.0 tensorflow/py27/1.11 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.12.0 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 1.3.1 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/py36/1.4 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/py27/1.4 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.5.0 tensorflow/py36/1.5 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.5.0 tensorflow/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 1.7.0 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-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 1.5.0 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/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/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/py36/1.7 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/py27/1.7 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
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 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/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 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.
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/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.
tmhmm 2.0c tmhmm/2.0c None application computational biology TMHMM 2.0 predicts transmembrane helices in proteins.
tophat 2.0 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.
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.
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.
tricubic 1.0 tricubic/1.0 compiler/gcc/4.9 library runtime support
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.
trilinos 12.6 trilinos/12.6 compiler/gcc/4.9:openmpi/1.10 library runtime support
trim_galore 0.4.0 trim_galore/0.4 None application computational biology Trim sequences
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
trinity 2.0 trinity/2.0 compiler/gcc/4.8 application computational biology Trinity RNA-Seq de novo transcriptome assembly
trinity 2.1 trinity/2.1 compiler/gcc/4.8 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 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 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.
turbowave 3.3 turbowave/3.3 compiler/intel/16:openmpi/1.10 application Physics
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-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 2.1 udunits2/2.1 compiler/gcc/4.7 compiler/pgi/14 compiler/pgi/15 compiler/intel/12 compiler/pgi/12 compiler/intel/13 compiler/pgi/13 compiler/gcc/4.8 library runtime support
udunits2 2.2 udunits2/2.2 compiler/pgi/12 compiler/intel/15 compiler/pgi/15 compiler/intel/16 compiler/pgi/13 compiler/intel/13 compiler/pgi/14 library runtime support
unicycler 0.4.7 unicycler/0.4 None application bioinformatics Hybrid assembly pipeline for bacterial genomes
upcr 2.20 upcr/2.20 compiler/gcc/4.9:openmpi/1.8 application compiler
upcr 2.24 upcr/2.24 compiler/gcc/5.4:openmpi/2.0 application compiler
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 2.4.3 varscan/2.4 None application computational biology Variant calling and somatic mutation/CNV detection for next-generation sequencing data
vasp 5.4 vasp/5.4sol compiler/intel/15:openmpi/2.1 library runtime support
vasp 5.4 vasp/5.4 compiler/intel/13:openmpi/1.8 library runtime support
vasp 5.4.4 vasp/5.4.4 compiler/intel/15:openmpi/2.1 library runtime support
vcftools 0.1 vcftools/0.1 None application computational biology VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
velvet 1.2 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.
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.
vim 8.1.0960 vim/8.1 None application Utility Vim is a greatly improved version of the good old UNIX editor Vi
virema 0.6 virema/0.6 None application computational biology
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.
vsearch 2.10.0 vsearch/2.10 None application computational biology A versatile open source tool for metagenomics (USEARCH alternative)
wevote 1.8 wevote/1.8 None library runtime support
wgrib2 2.0.6 wgrib2/2.0 None application file processing wgrib2 is more like four drawers of kitchen utensils as well as the microwave and blender.
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.
xpclr 1.0 xpclr/1.0 None application computational biology detecting selective sweeps via the differentiation of two populations
xzutils 5.2 xzutils/5.2 None 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/pgi/12 compiler/pgi/14 compiler/intel/15 compiler/intel/13 compiler/pgi/13 compiler/intel/12 compiler/pgi/15 compiler/intel/16 None compiler/gcc/4.9 compiler/intel/18 compiler/gcc/4.8 compiler/gcc/4.7 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.