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Alces Gridware Software Applications

This page documents the software which is currently available via the Alces Gridware project. Software applications are listed in the Alces Gridware repository with the structure repository/type/name/version, which corresponds to:

  • repository - packages are listed in the main repository if available for auto-scaling clusters, and the volatile repository otherwise.
  • type - packages are listed as apps (applications), libs (shared libraries), compilers or mpi (message-passing interface API software for parallel applications)
  • name - the name of the software package
  • version - the published version of the software package

For example, a package listed as main/apps/bowtie2/2.2.6 is version 2.2.6 of the Bowtie2 application, from the stable repository.

The following list is updated periodically as new software is added to the repositories. For clarity, multiple versions of the same application are not shown, unless there are significant functional differences between versions. Software categories are provided as a guide only - many packages are multi-discipline and have a range of appropriate uses.

Tools and Utilities

gnuplot         A portable command-line driven graphing utility
grace           Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif
idr             Framework to measure the reproducibility of findings
mawk            mawk is an interpreter for the AWK Programming Language.
parallel        A shell tool for executing jobs in parallel using one or more computers


HPL             A Portable Implementation of the High-Performance Linpack Benchmark for Distributed-Memory Computers
memtester       A userspace utility for testing the memory subsystem for faults.
hpcc            The HPC Challenge benchmark
imb             IMB is a networking benchmark tool.
iozone          IOzone is a filesystem benchmark tool.
gpuburn         GPU-Burn is a stress test for multi-GPGPU-setups.
Folding@home    A distributed computing project studying protein folding and misfolding


amber           Set of programs for biomolecular simulation and analysis
beast           Cross-platform program for Bayesian MCMC analysis of molecular sequences
placement       An algorithm for prediction of explicit solvent atom distribution


MS Prot Tools   Some hopefully useful tools for mass spectrometry applied to proteomics
454 Sequencing  454 Sequencing System Off-Instrument Software Applications suite
ABRA            Assembly Based ReAligner
'AbySS          A de novo, parallel, paired-end sequence assembler that is designed for short reads
ANGES           Reconstucts ancestral genome maps from homologous markers in extant related genomes
ANNOVAR         Functional annotation of genetic variants from high-throughput sequencing data
ARAGORN         Detect tRNA genes and tmRNA genes in nucleotide sequences
ArtificialFqG   Ouputs artificial FASTQ files derived from a reference genome
Atlas-SNP2      Next-generation sequencing suite of variant analysis tools
AUGUSTUS        Predicts genes in eukaryotic genomic sequences
autoadapt       Automatically detect and remove adaptors and primers present in a FASTQ file
bam-readcount   Generate metrics at single nucleotide positions
BAMStats        Tool to calculate and display various metrics derived from SAM/BAM files
BamTools        Provides a programmer's API and an end-user's toolkit for handling BAM files
bamUtil         Several programs that perform operations on SAM/BAM files
BamView         Interactive display of read alignments in BAM data files
BLAST           Compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches
Batalign        An incremental method for accurate gapped alignment
BCFtools        Utilities for variant calling and manipulating VCF and BCF files
Bcl2FastQ       A tool to handle bcl conversion and demultiplexing
Bcl2FastQ       A tool to handle bcl conversion and demultiplexing
BCL Converter   Convert *.bcl files into *_qseq.txt files
BEAGLE          A general purpose library for evaluating the likelihood of sequence evolution on trees
BEAGLE          Analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples
BEAGLE          A general purpose library for evaluating the likelihood of sequence evolution on trees
BEDTools        A flexible suite of utilities for comparing genomic features
biom-format     The Biological Observation Matrix (BIOM) format
BIONJ           An improved version of the NJ algorithm based on a simple model of sequence data
BioPerl         A community effort to produce Perl code which is useful in biology
Biopython       Set of freely available tools for biological computation written in Python
bio-rainbow     Package for RAD-seq related clustering and de novo assembly.
Bismark         A bisulfite read mapper and methylation caller
BLAST (Legacy)  Compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches
Bowtie 2        Fast and sensitive read alignment
Bowtie          Ultrafast memory-efficient short read aligner
BreakPointer    Pinpoint rearrangement breakpoints using paired end reads
CAP3            Sequence Assembly Program
car             Reconstructing contiguous regions of an ancestral genome
cdbfasta        CDB (Constant DataBase) indexing and retrieval tools for FASTA files
CD-HIT          A program for clustering DNA/protein sequence database at high identity with tolerance.
cdhit           A program for clustering and comparing protein or nucleotide sequences.
CEGMA           Building sets of gene annotations in eukaryotic genomes
CGAT            The Computational Genomics Analysis Toolkit
CHANCE          Assess the quality of ChiP-seq experiments
CHIAMO          Call genotypes from the Affymetrix 500K Mapping chip
Chimerascan     Detection of chimeric transcripts in high-throughput sequencing data
ClonalFrame     Inference of bacterial microevolution using multilocus sequence data
CLUMPP          Deals with label switching and multimodality problems in population-genetic cluster analyses
Clustal Omega   Multiple alignment of nucleic acid and protein sequences
ClustalW        Multiple alignment of nucleic acid and protein sequences
cnD             Copy number variant caller for inbred strains
CNVnator        CNV discovery and genotyping from depth of read mapping
CoNIFER         Copy Number Inference From Exome Reads
CASAVA          Processes sequencing reads provided by RTA or OLB
CONTIGuator     A bacterial genomes finishing tool for structural insights on draft genomes
Control-FREEC   Detect copy-number changes and allelic imbalances using deep-sequencing data
CNATR           Tool for copy number variation (CNV) detection for targeted resequencing data
Corset          Software for clustering de novo assembled transcripts and counting overlapping reads
Cortex          "Software for genome assembly and variation analysis
CRAMTools       Set of Java tools and APIs for efficient compression of sequence read data
CREST           Algorithm for detecting genomic structural variations at base-pair resolution
CRISP           Multi-sample variant caller for high-throughput pooled sequence data
Curtain         Assembler of next generation sequence, developed by Matthias Haimel in the Ensembl Genomes team at the EBI
cutadapt        A tool that removes adapter sequences from DNA sequencing reads
DARWIN          Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences
DDiMAP          Analyses mapped NGS read data to discover rare variants
dDocent         An interactive bash wrapper to QC, assemble, map, and call SNPs from double digest RAD data
Delly           Structural variant discovery by integrated paired-end and split-read analysis
distruct        Graphically display results produced by the genetic clustering program structure
DREEP           Detecting low-level mutations by utilizing the RE-sequencing Error Profile of the data
EAD             Error aware demultiplexer is a probabilistic demultiplexer for Illumina BCL files.
EIGENSOFT       Combines functionality from population genetics methods and EIGENSTRAT stratification method
EIGENSOFT       Combines functionality from population genetics methods and EIGENSTRAT stratification method
Ensembl API     Abstraction layer for accessing Ensembl genomic databases
Ensembl Variant Effect Predictor        Predict the functional consequences of known and unknown variants
e-PCR           Identifies sequence tagged sites (STSs) within DNA sequences
Exonerate       Generic tool for pairwise sequence comparison
eXpress         Streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences
FamSeq          A computational tool for calculating probability of variants in family-based sequencing data
FASTA           Search protein or DNA sequence databases comparing a protein sequence to a DNA sequence database
FastQC          A quality control tool for high throughput sequence data
fastq-tools     Small utilities for working with fastq sequence files
FastTree        Inference of approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
FastUniq        an ultrafast de novo duplicates removal tool for paired short DNA sequences
Flexbar         Flexible barcode and adapter removal for sequencing platforms
FreeBayes       Bayesian genetic variant detector designed to find small polymorphisms
FREGENE         Simulates sequence-like data over large genomic regions in large diploid populations
FusionFinder    Find fusion transcript candidates in RNA-Seq data
FusionMap       Align reads spanning fusion junctions directly to the genome
Galaxy          Open, web-based platform for data intensive biomedical research
GBrowse         The Generic Genome Browser
geneid          Predicts genes in anonymous genomic sequences designed with a hierarchical structure
GeneTorrent     Transfer genomic data reliably across a network
GATK            Software package developed at the Broad Institute to analyse next-generation resequencing data
GAT + queue     Broad Institute package for analysing next-generation resequencing data; including command-line scripting framework for defining multi-stage genomic analysis pipelines
GenomeMapper    Short read mapping tool designed for accurate read alignments
GENSCAN         Analyze genomic DNA sequences from a variety of organisms
GERP++          Identifies constrained elements in multiple alignments by quantifying substitution deficits
GIMSAN          GIbbsMarkov with Significance ANalysis
Glimmer         System for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses
GMAP/GSNAP      Genomic mapping and alignment and short-read nucleotide alignment programs
GREAT           Genomic Regions Enrichment of Annotations Tool
Grinder         A versatile omics shotgun and amplicon sequencing read simulator
GTOOL           Transforms sets of genotype data for use with the programs SNPTEST and IMPUTE
HAL             Hierarchical Alignment Format API and analysis and conversion tools
hapflk          Haplotype-based test for differentiation in multiple populations
HLA*IMP BE      Impute HLA type information based on SNP genotypes back-end
HLA*IMP FE      Impute HLA type information based on SNP genotypes front-end
HMMcopy         Make copy number estimations for whole genome data
HPCall          Improved base-calling for homopolymer-sensitive next-gen data
HTSeq           Process data from high-throughput sequencing assays
HTSlib          C library for high-throughput sequencing data formats
abacas          Rapidly contiguate (align, order, orientate), visualize and design primers
Bio-bwa         Aligns relatively short nucleotide sequences against a long reference sequence such as the human genome
bowtie2         Fast and sensitive read alignment
bowtie          Ultrafast memory-efficient short read aligner
bedtools        A flexible suite of utilities for comparing genomic features
phast           Software package for comparative and evolutionary genomics
cufflinks       Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
emboss          Software analysis suite developed for the molecular biology community
genetics        Reports position-specific measures of conservation
genome          An alignment tool like BLAST
varscan         Mutation caller for targeted, exome, and whole-genome resequencing data
breakdancer     Provides genome-wide detection of structural variants from next generation paired-end sequencing reads
Genome-music    A comprehensive analysis suite for mutations in cancer genomes
radmarkers      Guppy RAD tools
fastx           A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing
fastx2          Assaf Gordon text utilities
hmmer           Biosequence analysis using profile hidden Markov models
htsfilter       Standard Filter for identification of polyclonal and independant errors for SOLiD short read sequences
macs            Novel algorithm for identifying transcript factor binding sites
sambamba        Tools for working with SAM/BAM data
mag             Builds qassembly by mapping short reads to reference sequences
picard          Java-based command-line utilities and API for manipulating SAM files
ribopicker      Identify and remove rRNA sequences from metagenomic and metatranscriptomic datasets
samtools        Provides various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format
plinkseq        Library for working with human genetic variation data
bamview         Variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format
recon           Package for finding repeat families from biological sequences
Picard-broad    Command line tools for manipulating high-throughput sequencing (HTS) data and formats
mabkit          Tools for common BAM file manipulations
speedseq        A flexible framework for rapid genome analysis and interpretation
fgwas           Functional genomics and genome-wide association studies
lighter         Fast and memory-efficient sequencing error corrector
bamtools3       Provides a programmer's API and an end-user's toolkit for handling BAM files
diffreps        Differential analysis for ChIP-seq with biological replicates
Macs-taoliu     Novel algorithm for identifying transcript factor binding sites
sift            Predicts whether an amino acid substitution affects protein function
impute          A genotype imputation and phasing program based on ideas from Howie et al. (2009)
snpomatic       Fast, stringent short-read mapping software
soap            A short read de novo assembly tool
amos            A collection of tools and class interfaces for the assembly of DNA reads
bfast           Facilitates the fast and accurate mapping of short reads to reference sequences
kggseq          A biological knowledge-based mining platform for genomic and genetic studies using sequence data
passion         A pattern growth algorithm based pipeline for splice site detection in paired-end RNA-Seq data
Cnv-seq         A method for detecting DNA copy number variation (CNV) using highthroughput sequencing
tophat          A spliced read mapper for RNA-Seq
Tophat-fusion   Enhanced version of TopHat with the ability to align reads across fusion points
trinitymaseq    A novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
vcftools        Package designed for working with VCF files, such as those generated by the 1000 Genomes Project
fastq_screen    A screening application for high throughput sequence data
gatk            Software package developed at the Broad Institute to analyse next-generation resequencing data
igv             A high-performance visualization tool for interactive exploration of large, integrated genomic datasets
scripture       Java-based command-line tool for transcriptome reconstruction
bertone         Subdivision of ChIP-seq/ChIP-chip regions into discrete signal peaks
oases           De novo transcriptome assembler for very short reads
velvet          Sequence assembler for very short reads
hgsc            SNP discovery tool developed for next generation sequencing platforms
illuminautils   File utilities for Illumina sequencers
htslib          Provides various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format
bam2fastq       Extract raw sequences (with qualities)
mothur          Provides microbial ecologists with the functionality of dotur, sons, treeclimber, s-libshuff, unifrac and more.
mutationtaster  Next-generation sequencing pipeline from Mutation Taster (http
ngsqctoolkit    A toolkit for the quality control (QC) of next generation sequencing (NGS) data
w.cgi           Software for performing Bayesian inference Using Gibbs Sampling
repeatmasker    Screens DNA sequences for interspersed repeats and low complexity DNA sequences
artemis         Genome browser and annotation tool
dindel          Calls small indels from next-generation sequence data by realigning reads to candidate haplotypes
reapr           Evaluates the accuracy of a genome assembly using mapped paired end reads
smalt           Efficiently aligns DNA sequencing reads with genomic reference sequences
shapeit         Segmented HAPlotype Estimation and Imputation Tool - Fast and accurate haplotype inference
stampy          Maps short reads from Illumina sequencing machines on to a reference genome
iassembler      Assemble ESTs generated using Sanger and/or Roche-454 pyrosequencing technologies into contigs
Infernal        Search DNA sequence databases for RNA structure and sequence similarities
InterProScan    Allows sequences to be scanned against InterPro's signatures
JAGS            Analysis of Bayesian hierarchical models using Markov Chain Monte Carlo simulation
Kent src utils  Jim Kent and the UCSC Genome Bioinformatics Group program suite
khmer           k-mer counting, filtering and graph traversal
LASTZ           Program for aligning DNA sequences, a pairwise aligner
LifeScope       LifeScope Genomic Analysis Solutions Tools
LOCAS           Low-coverage short-read assembler
LoFreq          Fast and sensitive variant-caller for inferring SNVs from high-throughput sequencing data
LUMPY           A probabilistic framework for structural variant discovery
MAFFT           Multiple alignment program for amino acid or nucleotide sequences
mafJoin         Tool for combining pairs of maf files that share a common sequence
MAKER           Portable and easily configurable genome annotation pipeline
M.A.Q Viewer    Graphical read alignement viewer
MaSuRCA         Whole genome assembly
Mauve           Mauve Genome Alignment Software
MeDUSA          Methylated DNA Utility for Sequence Analysis - Computational pipeline to perform a full analysis of MeDIP-seq data
MEGA            Molecular Evolutionary Genetics Analysis - Software suite for analyzing DNA and protein sequence data from species and populations
MEME Suite      Motif-based sequence analysis tools
MERLIN          Uses sparse trees to represent gene flow in pedigrees
Microbiome      Microbiome Utilities
MIRA            Whole genome shotgun and EST sequence assembler
MISO            Probabilistic analysis and design of RNA-Seq experiments for identifying isoform regulation
MitoSeek        Extraction of mitochondrial genome information from exome sequencing data
MODELLER        Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Results
mpiBLAST        Open-Source Parallel BLAST
MrBayes         Bayesian Inference of Phylogeny
Multiz/TBA      Threaded-Blockset Aligner, a local multiple sequence alignment tool; MULTIZ, aligns highly rearranged or incompletely sequenced genomes
MUMmer          System for rapidly aligning entire genomes
MUSCLE          Multiple sequence alignment
MuTect          Reliable and accurate identification of somatic point mutations
NGS-SNP         Collection of command-line scripts for providing rich annotations for SNPs
Novoalign       Aligner for short nucleotide space reads
NucleoATAC      Package for calling nucleosomes using ATAC-Seq data
Oases           De novo transcriptome assembler for very short reads
454-OISA        454 Sequencing System Off-Instrument Software Applications suite
OL Basecaller   Performs base calling and bcl to qseq conversion for the HiSeq, HiScan-SQ, or Genome Analyzer
ONCOCNV         Detection of copy number changes in Deep Sequencing data
OncoSNP-SEQ     Characterise copy number alterations and loss-of-heterozygosity events
Oncotator       Annotate human genomic point mutations and indels with data relevant to cancer researchers
OpenMS          LC/MS data management and analyses
PAGIT           Post Assembly Genome Improvement Toolkit
PAML            Phylogenetic Analysis by Maximum Likelihood
Panseq          Determine the core and accessory regions among a collection of genomic sequences
PeakRanger      Multi-purporse software suite for analyzing next-generation sequencing (NGS) data
PEAR            PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger
PeSV-Fisher     Pipeline for the detection of five general types of structural variants
phantompeakqual Compute quick, highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data
phrap           phrap is a program for assembling shotgun DNA sequence data
PHYLIP          A free package of programs for inferring phylogenies
Pindel          Detection of breakpoints of structural variants at single-based resolution from next-gen sequence data
plink           Whole genome association analysis toolkit
Polymutt        Calls single nucleotide variants and detects de novo point mutation events in families for next-generation sequencing data
PolyPhen-2      Predicts possible impact of amino acid substitutions on the structure and function of human proteins
popoolation2    Allows comparision of allele frequencies between two ore more populations
popoolation     Estimate natural variation and positive selection
Preseq          Predict and estimate the complexity of a genomic sequencing library
Primer3         PCR primer design tool
PRINSEQ Lite    Filter, reformat, or trim genomic and metagenomic sequence data
PROCHECK        Stereochemical protein structure quality analysis
ProgCactus      A whole-genome alignment package
PSIPRED         Accurate protein secondary structure prediction
PyCogent        A toolkit for making sense from sequence
PyNAST          Python Nearest Alignment Space Termination tool
pyprophet       Analyse MRM data
PyroBayes       A novel base caller for pyrosequences from the 454 Life Sciences sequencing machines
Q               Whole genome association analysis toolkit
Qiime           Quantitative Insights Into Microbial Ecology
RAxML           Randomized Axelerated Maximum Likelihood        Sequential and parallel inference of large phylogenies with maximum likelihood
Rcount          Simple and flexible RNA-Seq read counting
RDP Classifier  Naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus.
RepeatNet       An ab initio centromeric sequence detection algorithm
rMATS           Detect differential alternative splicing events from RNA-Seq data
RMBlast         NCBI Blast modified for use with RepeatMasker/RepeatModeler
RSEM            Estimate gene and isoform expression levels from RNA-Seq data
RSeQC           An RNA-seq Quality Control Package
RStudio Desktop A free and open source integrated development environment for R
samblaster      Mark duplicates and extract discordant and split reads from sam files
Satsuma         High-sensitivity alignments through cross-correlation
screed          Short read sequence utils in Python.
Scythe          A very simple adapter trimmer
Scythe          A very simple adapter trimmer
SeqAn           Open source C++ library of efficient algorithms and data structures for the analysis of sequences
SeqClean        The Gene Indices Sequence Cleaning and Validation script (SeqClean)
SeqEM           Adaptive genotype-calling approach for next-generation sequencing studies
SeqGene         Software for mining next-gen sequencing datasets
Seqtk           Toolkit for processing sequences in FASTA/Q formats
SRAT            Programmatically access data housed within SRA and convert it from the SRA format
SSAHA           Sequence Search and Alignment by Hashing Algorithm - A pairwise sequence alignment program for efficient mapping of sequencing reads
SVA             Sequence Variant Analyzer - Annotate, visualize and analyze the genetic variants indentifed through next-generation sequencing studies
SOAP            Short Oligonucleotide Analysis Package - An updated version of SOAP software for short oligonucleotide alignment
SHRiMP          Software package for aligning genomic reads against a target genome
SICER           Identify enriched domains from histone modification ChIP-Seq data
Sickle          A windowed adaptive trimming tool for FASTQ files using quality
Sickle          A windowed adaptive trimming tool for FASTQ files using quality
Sierra Perl     Perl client to access Sierra, the Stanford HIV Web Service
SiPhy           Rigorous statistical tests to detect bases under selection from a multiple alignment data
SNAP            General purpose gene finding for both eukaryotic and prokaryotic genomes
snpEff          Fast variant effect predictor (SNP, MNP and InDels) for genomic data
SNPTEST v2      Analysis of single SNP association in genome-wide studies
SNVMix          Detect single nucleotide variants from next generation sequencing data
SOAPdenovoTrans A de novo transcriptome assembler designed specifically for RNA-Seq
SOAPfusion      Fusion discovery with paired-end RNA-Seq reads
SOAP-ICLU       Identify genome-wide large variants, such as CNVs and LOH etc.
'SOAPIndel'     Call indels from next-generation paired-end sequencing data
SOAPsnp         Calls consensus genotype by carefully considering data quality, alignment and recurring experimental errors
'SOAPsplice'    Genome-wide ab initio detection of splice junction sites from RNA-Seq
STIR            Software for Tomographic Image Reconstruction - Multi-platform object-oriented framework for data manipulations in tomographic imaging
SortMeRNA       SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatranscriptomic data produced by next-generation sequencers.
Stacks          Software pipeline for building loci from short-read sequences
Staden Package  A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin)
STAR            Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays
Strelka         Somatic variant calling workflow for matched tumor-normal samples
StructHarvester Extracting data from STRUCTURE results files
Structure       Use multi-locus genotype data to investigate population structure
SuperHirn       Tool to quantitatively analyze multi-dimensional LC-MS data
SVMerge         Enhanced structural variant and breakpoint detection
Tabix++         C++ wrapper to Tabix indexer for TAB-delimited genome position files
Tabix           Generic indexer for TAB-delimited genome position files
Tablet          Lightweight, high-performance graphical viewer for next generation sequence assemblies and alignements
Tandem Repeats  Locate and display tandem repeats in DNA sequences
tax2tree        Assists in decorating an existing taxonomy onto a phylogenetic tree with overlapping tip names
T-Coffee        Align sequences or combine the output of other alignment methods into one unique alignment
TMAP            Torrent mapping alignment program
TopHat          A spliced read mapper for RNA-Seq
Trans-ABySS     Analyze ABySS multi-k-assembled shotgun transcriptome data
treeviewx       Phylogeny tree viewer
Trim Galore!    Wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files
Trimmomatic     A flexible read trimming tool for Illumina NGS data
Trinity         A novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
trRNAscan-SE    Improved detection of transfer RNA genes in genomic sequence
UNPHASED        Software for genetic association analysis
USeq            Collection of software tools for analysis of sequencing data from the Solexa, SOLiD, and 454 platforms
VariationHunter A tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies
vcflib utils    Command-line utilities for executing complex manipulations on VCF files
Velvet          Sequence assembler for very short reads
VerifyBamID     Verify whether reads match previously known genotypes for an individual
Vienna RNA      RNA Secondary Structure Prediction and Comparison
Vmatch          Software tool for efficiently solving large scale sequence matching tasks
Wise2           Program for aligning proteins or protein HMMs to DNA
WU BLAST        Washington University-produced alternative to NCBI BLAST
wwwblast        A suite of standalone BLAST programs produced by NCBI for use on the web
Bioconductor    Tools for the analysis and comprehension of high-throughput genomic data


vmd             Molecular visualization program for displaying, animating, and analyzing large biomolecular systems
molscript       MolScript is a program for displaying molecular 3D structures
NAMD            A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems
PyMOL           PyMOL is a Python-enhanced molecular graphics tool
RasMOL          RasMol is a program for molecular graphics visualisation


ASE             Atomistic Simulation Environment - Python modules for manipulating atoms, analyzing simulations and visualization
Desmond         High-speed molecular dynamics simulations of biological systems
DL_POLY         General purpose classical molecular dynamics (MD) simulation
ESPResSo        Extensible Simulation Package for Research on Soft matter
GAMESS          General Atomic and Molecular Electronic Structure System (GAMESS)  -Ab initio molecular quantum chemistry
babel           A chemical toolbox designed to speak the many languages of chemical data
gpaw            A density-functional theory (DFT) Python code
gromacs         Perform molecular dynamics; simulate the Newtonian equations of motion for systems with hundreds to millions of particles
nwchem          Methods for computing the properties of molecular and periodic systems
OpenMD          Open source molecular dynamics engine
Maestro         Schrodinger Maestro - a powerful, all-purpose molecular modelling environment


GNU GCC         GNU Compiler Collection including front ends for C, C++, Objective-C and Fortran
Cluster Studio  Intel Cluster Studio - High performance cluster tools to increase performance and scalability
Open64          An open source, optimizing compiler for the Itanium and x86-64 microprocessor architectures
Oracle Java(TM) Java Programing Language


hdf5            Data model, library, and file format for storing and managing data


Octopus         A scientific program aimed at the ab initio virtual experimentation


ANSYS Workbench Suite of advanced engineering simulation tools
Code_Saturne    Solve the Navier-Stokes equations for 2D, 2D-axisymmetric and 3D flows


GRASS GIS       Free and open source Geographic Information System (GIS) software suite
PROJ.4          Convert geographic longitude and latitude coordinates into cartesian coordinates

Graphics and Imaging

DIL             Developer's Image Library - Cross-platform image library utilizing a simple syntax to load, save, convert, manipulate, filter and display a variety of images with ease
POV-Ray         The Persistence of Vision Raytracer
vtk             Package for 3D graphics, modeling and image processing
Bsoft           Bernard's Software Package
CTFFIND3        CTF estimation
CTFFIND4        CTF estimation
Dynamo          Software environment for subtomogram averaging of cryo-EM data
EMAN2           Broadly based greyscale scientific image processing suite
FFmpeg          A complete, cross-platform solution to record, convert and stream audio and video
IHRSR++         Extension of Iterative Helical Real Space Reconstruction (IHRSR) software
IMOD            Image processing, modeling and display programs for tomographic reconstruction
RELION          REgularised LIkelihood OptimisatioN
ResMap          Local Resolution Map Algorithm
SPIDER          System for Processing Image Data from Electron microscopy and Related fields


Anaconda Py2.7  Completely free Python distribution including popular Python packages (python 2.7)
Anaconda Py3    Completely free Python distribution including popular Python packages (python 3)
Cython          C-Extensions for Python
Glasgow         Haskell Compiler and interactive environment for the functional language Haskell
julia           High-level, high-performance dynamic programming language for technical computing
perl            A highly capable, feature-rich programming language with over 24 years of development
php             A widely-used general-purpose scripting language that is especially suited for Web development
python          A remarkably powerful dynamic programming language
R               Language and environment for statistical computing and graphics
ruby            A dynamic, open source programming language with a focus on simplicity and productivity
IPython         Rich architecture for interactive computing, supporting Project Jupyter
Mono            A software platform designed to allow developers to easily create cross platform applications
Oracle Java(TM) Java Programing Language
R               Language and environment for statistical computing and graphics
Scala           Multi-paradigm programming language built on top of the Java virtual machine.
Virtualenv      Virtual Python Environment Builder


GCC             GNU C/C++ Compiler
ANTLR           ANother Tool for Language Recognition - Language tool that provides a framework for constructing interpreters, compilers, and translators
BLACS           Basic Linear Algebra Communication Subprograms - A linear algebra oriented message passing interface
Caffe           A fast open framework for deep learning
CUDA Toolkit    Development environment for C and C++ developers building GPU-accelerated applications
CythonGSL       Cython interface for the GNU Scientific Library (GSL)
GEOS            Geometry Engine, Open Source
GDAL            Geospatial Data Abstraction Library     Translator library for raster geospatial data formats
GMP             Library for arbitrary precision arithmetic
GSL             GNU Scientific Library - A numerical library for C and C++ programmers
Rnetcdf         RNetCDF
libdc1394       C++ API to the PostgreSQL database management system.
Math-atlas      Automatically Tuned Linear Algebra Software - portably optimal linear algebra software
mpi4py          Python bindings for the Message Passing Interface (MPI)
libgit2         Portable, pure C implementation of the Git core methods
boost           Free peer-reviewed portable C++ source libraries
fftw            C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions
fltk            A cross-platform C++ GUI toolkit providing modern GUI functionality without the bloat
freeds          A set of libraries for Unix and Linux that allow programs to natively talk to Microsoft SQL Server and Sybase databases
freetype        Freetype fonts package
graphicsmagick  Swiss army knife of image processing
imagemagick     An open source software suite for displaying, converting, and editing raster image files
Blas-forum      Reference implementation for the C interface to the Legacy BLAS
blas            Routines that provide standard building blocks for performing basic vector and matrix operations
clapack         LAPACK translated from Fortran to C
lapack          Linear Algebra PACKage - routines for equation solving systems
scalapack       A library of high-performance linear algebra routines for parallel distributed memory machines
pil             Adds image processing capabilities to your Python interpreter
netcdf          NetCDF
zeroc           A modern distributed computing platform.
Img             Support for many image formats for Tk
JasPer          Reference implementation of the JPEG-2000 Part-1 standard
Lasagne         Lightweight library to build and train neural networks in Theano
libctl          Flexible control files for scientific simulations
libgdiplus      C-based implementation of the GDI+ API
Libxc           Libxc is a library of exchange-correlation functionals for density-functional theory.
LLVM Core       A modern source- and target-independent optimizer with code generation support
matplotlib      2D plotting library for Python which produces publication quality figures
MPFR            C library for multiple-precision floating-point computations with correct rounding
NetCDF Fortran  Set of interfaces and libraries for array-oriented data access
NetCDF          Set of interfaces and libraries for array-oriented data access
numexpr         Fast numerical array expression evaluator for Python and NumPy
OpenBLAS        An optimized BLAS library
OpenCV          Open source computer vision and machine learning software library
OpenLibm        High quality, portable, standalone C mathematical library
pandas          Powerful data structures for data analysis, time series,and statistics
PCRE2           Perl Compatible Regular Expressions
Protocol Buff   Protocol Buffers are a way of encoding structured data in an efficient yet extensible format. Google uses Protocol Buffers for almost all of its internal RPC protocols and file formats.
pybedtools      Wrapper around BEDTools for bioinformatics work
pythonlevenshtein Python extension for computing string edit distances and similarities
PyGTK Libraries GTK+ for Python
PyQt4           Python v2 and v3 bindings for Digia's Qt application framework
PyQwt           PyQwt plots data with Numerical Python and PyQt
Pysam           Python module for reading and manipulating Samfiles
PyTables        Hierarchical datasets
Qt              A cross-platform application and UI framework
QuTIP           Quantum Toolbox in Python
Rmpi            Provides an interface (wrapper) to MPI APIs
ROOT            Set of OO frameworks to handle and analyze large amounts of data efficiently
RPy             A simple and efficient access to R from Python
Seaborn         Seaborn is a Python visualization library based on matplotlib.
SLICOT          Subroutine Library in Systems and Control Theory
Snappy Java     Snappy compressor/decompressor for Java
snpsites        Rapidly extract SNPs from a multi-FASTA alignment
SparseHash      An extremely memory-efficient hash_map implementation
SPIOL           Staden Package I/O Libraries - I/O libraries developed as part of the Staden Project
Theano          Define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently
TBB             Threading Building Blocks - C++ template library that simplifies the development of software applications running in parallel
Trilinos        Algorithms for the solution of multi-physics engineering and scientific problems
UDUNITS         Programatic handling of units of physical quantities
Ceres Solver    C++ library for modeling and solving large complicated nonlinear least squares problems
GetPot          Tool to parse the command line and configuration files.
gflags          Library that implements commandline flags processing
glog            Application-level logging library
nanoflann       C++ header-only fork of FLANN, a library for KD-trees
pyBigWig        A python extension, written in C, for quick access to and creation of bigWig files.


eigen           C++ template library for linear algebra
Arpack-ng       Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems
numpy           Fundamental package for scientific computing in Python
suitesparse     A suite of sparse matrix packages
octave          High-level interpreted language, primarily intended for numerical computations
qhull           General dimension code for computing convex hulls
GCAL            Computational Geometry Algorithms Library
METIS           Serial Graph Partitioning and Fill-reducing Matrix Ordering
MGRIDGEN        Obtain a sequence of successive coarse grids that are well-suited for geometric multigrid methods
qrupdate        Fortran library for fast updates of QR and Cholesky decompositions
SciPy           Scientific tools for Python
SCOTCH          Graph and mesh/hypergraph partitioning, graph clustering, and sparse matrix ordering
SMLT            The Shogun Machine Learning Toolbox - A large scale machine learning toolbox


FreeSurfer      A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data
FreeSurfer      An open source software suite for processing and analyzing (human) brain MRI images


mvapich2        MPI-2 over OpenFabrics-IB, OpenFabrics-iWARP, PSM, uDAPL and TCP/IP
mvapich         MPI-1 over OpenFabrics/Gen2, OprnFabrics/Gen2-UD, uDAPL, InfiniPath, VAPI and TCP/IP
mpich2          A high-performance and widely portable implementation of the MPI standard (both MPI-1 and MPI-2)
MPICH           A high-performance and widely portable implementation of the MPI standard (MPI-1, MPI-2 and MPI-3)
Open MPI        A High Performance Message Passing Library


CASTEP          A leading code for calculating the properties of materials from first principles
fREEDA          Multi-physics simulator
Harminv         Extract mode frequencies from time-series data
openfoam        A C++ toolbox for the development of customized numerical solvers, and pre-/post-processing utilities
LAMMPS          Molecular Dynamics Simulator - LAMMPS ('Large-scale Atomic/Molecular Massively Parallel Simulator') is a molecular dynamics program from Sandia National Laboratories
Meep            Finite-difference time-domain (FDTD) simulation software
MPB             MIT Photonic Bands - Electromagnetic eigenmode solver


biogeme         Estimation of discrete choice models
fastlowess      An improved version of statsmodel's lowess
GGPlot          An implementation of the grammar of graphics in R


Bazel           Correct, reproducible, fast builds for everyone
bcrypt          Cross-platform file encryption utility
CMake           An extensible, open-source system that manages the build process in an operating system and compiler-independent manner
EC2 AMI Tools   Command-line tools to create and manage Amazon Machine Images
EC2 API Tools   Command-line tools for managing EC2 instances
Git             Git - the stupid content tracker
GNU Parallel    Shell tool for executing jobs in parallel using one or more computers
flex            The fast lexical analyzer
cpanminus       Get, unpack, build and install modules from CPAN
patchelf        Utility to modify the dynamic linker and RPATH of ELF executables
cmake           An extensible, open-source system that manages the build process in an operating system and compiler-independent manner
tau             Portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python
OpenStackClient Command-line client for OpenStack
pip             The PyPA recommended tool for installing and managing Python packages.
setuptools      Download, build, install, upgrade and uninstall Python packages -- easily!
SIP             Automatically generate Python bindings for C and C++ libraries
h5utils         Utilities for visualization and conversion of scientific data in HDF5 format
mbuffer         Tool for buffering data streams


Circos          A software package for visualizing data and information.
ants            Advanced Normalization ToolS for brain and image mapping
OctoMap         A probabilistic, flexible, and compact 3D mapping library for robotic systems
ParaView        Data analysis and visualization