CIS Computing & Information Services

Software (old list)

A key benefit of using CCV's computing resources is that we install and maintain a large collection of computational research software. We can install most software packages upon request and many popular packages are already available, including:


MATLAB (by MathWorks), is a numerical computing environment useful for performing numerical computations with matrices and vectors, data visualization (e.g. plotting of functions and data), and implementation of models and algorithms. It can also interface with programs written in other languages, including C, C++, Java, and Fortran.


Python is a general-purpose programming language with a design philosophy that emphasizes code readability. Its efficient high-level data structures and approach to object-oriented programming makes it an easy to learn, powerful programming language. Altogether, Python is an ideal language for scripting and rapid application development.


R is a programming language and environment for statistical computing and graphics. The R language is widely used among statisticians and data miners to analyze data and develop applications.

High-Performance Computing

PyModules, an alternative implementation of the Environment Modules system for managing software environments on research computing clusters.

MPI (Message Passing Interface)

Standard C and Fortran do not have constructs that support parallelism.
The Message Passing Interface (MPI) was developed as a standard using commonly-available operating system services to create parallel processes and exchange information among these processes.

Alphabetical List of Selected Software installed at CCV

command:Name - description

abaqus:Abaqus - Finite Element Analysis
abyss:ABySS - A De Novo, Parallel, Paired-end Sequence Assembler
acml:ACML - AMD Core math Library
adndp:AdNDP - Adaptive Natural Density Partitioning
afni:AFNI - Analysis of Functional Neuro Images
agalma:Agalma - Automated Transcriptome Assembly Pipeline
ale:ALE - Assembly Likelihood Estimator
ambertools:AmberTools - Assisted Model Building with Energy Refinement, molecular dynamics package
amdis:AmDiS - Adapative MultiDimensional Simulations
amos:AMOS - A Modular, Open-Source whole genome assembler
amphora2: MPHORA is an automated phylogenomic inference application for large-scale protein phylogenetic analysis.
annovar:ANNOVAR - functional annotation of genetic variants
ansys:ANSYS - Electroncs simulation Software including HFSS (Licensed by Engineering)
ants:ANTS - Advanced Normalization Tools
arb:ARB - Sequence Database Handling and Data Anaylsis
ase:ase - Atomic Simulation Environment
aspera:Aspera Connect - High Performance Transfer Client
atlas:ATLAS (Automatically Tuned Linear Algebra Software)`
atomeye:AtomEye - atomistic configuration viewer
augustus:augustus - gene prediction for eukaryotes
avida:Avida - Digital Evolution platform
b2g4pipe:B2G4PIPE - A version for B2G annotation without FrontEnd (GUI) for Pipeline Integration
bamtools:BamTools - Toolkit for BAM Alignment Files
bbmap:BBMap - A short read aligner
bcftools:BCFtools - utilities for variant calling and manipulating VCFs and BCFs (part of samtools)
beagle:Beagle - evaluate the likelihood of sequence evolution on trees
beast:BEAST - Bayesian MCMC Analysis of Molecular Sequences
bedops:bedops - Tools for genomics data
bedtools:BEDTools - Flexible suite of utilities for comparing genomic features
bellmansgapc:Bellman’s GAP Compiler - an ADP compiler which translates GAP-L programs into efficient C++ code
bib:bib - Bioinformatics Brew
bigdft:DFT - massively parallel electronic structure code
biol1425:Scripts for course BIOL1425
biolite:BioLite - bioinformatics workflows with provenance and diagnostics
biomed:biomed - some handy customized scripts for bioinformatics
bits:BITS - binary interval search with CUDA
blas:blas - Basic Linear Algebra Subprograms
blasr:BLASR - long read aligner
blast:BLAST - Basic Local Alignment Search Tool
blat:Blat is an alignment tool like BLAST
blender:Blender 3D render package
boost:Boost - The Boost C++ Libraries
bowtie:Bowtie - An ultrafast memory-efficient short read aligner
bowtie2:Bowtie2 - Fast and sensitive read alignment
breakdancer:breakdancer - SV detection from paired end reads mapping
bsmap:BSMAP is a short reads mapping software for bisulfite sequencing reads.
busco:BUSCO - Completeness Assessment for genome assemblies
bwa:BWA - Burrows-Wheeler Aligner
bxh_xcede_tools:BXH-XCEDE tools
c3d:C3d - Convert3d Medical Image Processing Tool
cadence:Cadence - EDA Software and Verification Tools
calculix:Calculix - 3D Structural Finit Element Program
calypso:Calypso - Crystal Structure Analysis by Particle Swarm Optimization
cantera:Cantera: A suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes.
casava:CASAVA - Genome Analyzer Software
cave:CAVE - everything you need for spelunking
cbsbio:Locating proteins in the cell using TargetP, SignalP, and related tools
cctools:Cooperative Computing Tools (cctools) - a collection of programs designed to assist users with the difficulties of building and
managing complex, fault-prone distributed systems
cd-hit:CD-HIT - clustering and comparing protein or nucleotide sequences
cegma:CEGMA - a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome
celera:Celera - Whole-Genome Shotgun Assembler
centos-libs:CentOS Libraries
centos-updates:Updated versions of programs include in CentOS
cgal:CGAL - Computing Genome Assembly Likelihoods
cgalorg:CGAL Computational Geometry Algorithms Library
chlororef:chlororef - Reference-Based Assembly Pipeline for Chloroplasts
circos:Circos - visualizes data in a circular layout
citcomcu:citcomCU - Finite element parallel code capable of modeling thermochemical convection in a three dimensional domain appropriate for convection within the Earth's mantle.
citcoms:citcomS - Finite element code designed to solve compressible thermochemical convection problems relevant to Earth's mantle.
clang:clang: a C language family frontend for LLVM
clang:libc++ included
clang:libc++ not included
clustal:Clustal - General Purpose Multiple Sequence Alignment Program for DNA or Proteins
clustalo: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.
cmake:CMake - Cross Platform Make
cnvnator:CNVnator - a tool for CNV discovery and genotyping from depth of read mapping
code-aster:code_aster - finite element library
comsol:COMSOL - Finite Element analysis sover (licensed by Engineering)
conifer: CoNIFER uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes.
consensus:Find DNA and protein patterns
coreutils:coreutils - the basic file, shell and text manipulation utilities of the GNU operating system
cosi:cosi - coalescent simulations
cppunit:cppunit - c++ port of JUnit framework
crossrate:crossrate - Chemical Kinetics and Dynamics Tools
cuda:CUDA - NVIDIA GPU Programming Toolkit
cudnn:cuDNN - NVIDIA CUDA Deep Neural Network library
cufflinks:Cufflinks - RNA Seq analysis tools
cutadapt:cutadapt - trim adapters from high-throughput sequencing reads
cytoscape: Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
dacapo-mva:Dacapo 2.7.16 using gfortran and mvapich2
datamash:datamash - a command-line program which performs basic numeric,textual and statistical operations on input textual data files
davinci:davinci - A tool to manipulate and view various types of data
dealii:deal.II - Finite Element Differential Equations Analysis Library
deconseq:deconseq - DECONtamination of SEQuence data using a modified version of BWA-SW
desmond:Desmond - molecular Dynamics System software
dftb+:DFTB+ - quantum mechanics simulation package
diamond:diamond - a BLAST-compatible local aligner for mapping protein and translated DNA query sequences
dicom-browser:DicomBrowser - an application for inspecting and modifying DICOM metadata in many files at once
dsrc:DSRC2 - Industry-oriented compression of FASTQ files
dwgsim:Whole genome simulation can be performed with dwgsim. dwgsim is based off of wgsim found in SAMtools written by Heng Li. It was modified to handle ABI SOLiD data, as well as various assumptions about aligners and positions of indels.
ea-utils:ea-utils - FASTQ processing utilities
ec2:Amazon EC2 API Tools
ecce:ECCE - PNNL Extensible Computational Chemistry Environment
edena:Edena - de novo short reads assembler
eeglab:EEGLAB - open source environment for electrophysiological signal processing
eigen:Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms
eigensoft:Eigensoft - genetics software
eloper:ELOPER - Elongation of paired-end reads for de novo assembly
emboss:EMBOSS - A collection of tools for molecular biology
emergent:Emergent - Neural Network Simulation System
enthought:Enthought Canopy is a comprehensive Python analysis environment
erne:ERNE - The Extended Randomized Numerical alignEr
esom:esom - Databionic ESOM tools
espresso:ESPResSo - Extensible Simulation Package for Research on Soft matter
exabayes:ExaBayes - Large Scale and Massively Parallel Bayesian Phylogenetic Inference
examl:ExaML - Exascale Maximum Likelihood for phylogenetic inference using MPI
exonerate:exonerate is a generic tool for pairwise sequence comparison.
express:eXpress - streaming quantification for high-throughput sequencing
falcon:FALCON - a set of tools for fast aligning long reads for consensus and assembly
fasta:FASTA - Sequence Comparison
fastqc:FastQC - Quality Control Application for Sequence Data
fastx-toolkit:FASTX-Toolkit - a collection of command line tools for FASTA/FASTQ files
fdtd:FDTD - 3d/2d maxwell solver
fenics:FEniCS, automated, efficient solution of differential equations
ferret:Ferret Data Visualization and Analysis
ffmpeg:FFmpeg - Audio and Video Convertor
fftw:The Fastest Fourier Transform in the West
fgap:FGAP - automated genome gap closing tool
fiji:Fiji - is just ImageJ
finis:FinIS - In silico assembly validation and finishing
firefox:Firefox - The web browser
fithic:Fit-Hi-C - a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome
architecture assays such as Hi-C
flash:FLASH - Fast Length Adjustment of SHort reads
fontconfig:fontconfig - library for configuring and customizing font access
freebayes:Freebayes - haplotype-based variant detector
freeglut:FreeGLUT - A completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library
freesurfer:FreeSurfer - Automated Tools for MRI Data
fsl:FSL - Analysis Tools for Brain Imaging Data
g3d:G3D - Open Source game engine, neede by vrg3d
ga:Global array 5.3 using intel compilers
gabedit:Gabedit: A Graphical User Interface to computational chemistry packages
gam-ngs:GAM-NGS - Genomic Assemblies Merger for NGS data
gapcloser:GapCloser - close gaps during genome scaffolding
gapfiller:GapFiller - De novo assembler to fill the gap within paired reads
gast:GAST - uses a reference database of SSU sequences to determine the taxonomy of hypervariable region tags
gatk:GATK - suite of tools for NGS data
gaussian:Gaussin v 09-c1 binary install from CD
gblocks:Gblocks - Selection of conserved blocks from multiple alignments
gcc:GCC - GNU Compiler Collection
gdal:GDAL - Geospatial Data Abstraction Library
gdb:GNU Debugger
geant:Geant4 - Particle Simulation Toolkit
geneid:geneid - a program to predict genes in anonymous genomic sequences designed with a hierarchical structure
genometools:GenomeTools - versatile open source genome analysis software
geos:GEOS - Geometry Engine, Open Source
getfem++:getfem++ finite element library
gfold:GFOLD - Generalized fold change for ranking differentially expressed genes from RNA-seq data
ghc:glasgow haskell compiler
ghostscript:An interpreter for the PostScript language and for PDF
gibbs:The Gibbs Motif Sampler will allow you to identify motifs, conserved regions, in DNA or protein sequences.
git:Git - Fast Version Control System
gmap-gsnap:GMAP and GSNAP: genomic alignment programs
gmin:GMIN - finding global minima and calculating thermodynamic properties from basin-sampling.
gmsh:gmsh - 3D Finite Element Mesh Generator
gnuplot:gnuplot - Graphing Utility
gpaw:GPAW - Grid-based projector-augmented wave method
gpaw-dip:GPAW - Grid-based projector-augmented wave method
gperftools:Google Performance Tools
grace:Grace Plotting and visualization tool
grads:GrADS - Grid Analysis and Display System
graphicsmagick:GraphicsMagick - Image Manipulation Library
graphviz:Graphviz - Graph Visualization Software
gromacs:GROMACS - mollecular dynamics program
groopm:GroopM - Automagical metagenomic binning
gsl:GSL - The GNU Scientific Library
gurobi:gurobi optimizer
h5utils:h5utils - Utilities for HDF5 files
hammer:Hammer - error correction with non-uniform coverage
hdf5:The Hierarchical Data Format v5
hdf5-par:The Hierarchical Data Format v5 (Parallel)
helisphere:HeliSphere - Open Source Bioinformatics Software
hic:A collection of tools to map, filter and analyze Hi-C data.
hiclib:hiclib - HiC correction library
hifix:HiFiX - HIgh FIdelity Clustering of Sequences
hmmer:HHMER - biosequence analysis using profile hidden Markov models
homer:Software for motif discovery and next generation sequencing analysis
hoomd-blue:hoomd-blue - general purpose particle simulation toolkit
hotbit:hotbit - charge-self-consistent density-functional tight-binding code
hpl:HPL - High-Performance Linpack Benchmark
humann2:HUMAnN2: The HMP Unified Metabolic Analysis Network 2
idba:IDBA - Iterative De Bruijn Graph De Novo Assembler
idr: IDR: Reproducibility and automatic thresholding of ChIP-seq data
igvtools:s package contains command line utilities for preprocessing, cottation feature count density (coverage), sorting, and indexing data files.
imagemagick:ImageMagick - Image Manipulation Library
intel:Intel Composer XE Compilers and MKL
interproscan:InterPro is an integrated database of predictive protein signatures used for the classification and automatic annotation of proteins and genomes
iraf:IRAF is the Image Reduction and Analysis Facility
isis:ISIS - Planetary Image Processing Software
JAGS:JAGS Just another Gibbs sampler
jasper: Jasper libraries for WRF
java:Java Developer's Kit (64-bit)
jellyfish:Fast, Parallel k-mer Counting for DNA
julia:Julia - high-level language for technical computing
kallisto:kallisto - near optimal rna-seq quantification
khmer:K-mer counting, filtering and graph traversal
kmergenie:KmerGenie - estimates best k-mer length for de novo assembly
kraken:Kraken - a taxonomic sequence classifier that assigns taxonomic labels to short DNA reads
lammps:LAMMPS - Molecular Dynamics Simulator
lapack:lapack - Linear Algebra PACKage
last:LAST - Genomic-scale sequence comparison
lastz:LASTZ - Improved pairwise alignment of genomic DNA
lemon: LEMON - Library for Efficient Modeling and Optimization in Networks
libpng:libpng compression for WRF
liggghts:LIGGGHTS - LAMMPS Improved for General Granular and Granular Heat Transfer Simulations
likwid:likwid - Lightweight Performance Tools
macs:MACS - Model-based Analysis for ChIP
macs:to run it please type: macs14 --help
macs:to run it please type: macs2 --help
macs:to run it please type: macs2 --help
macs:to run it please type: macs2 --help
mafft:MAFFT - Multiple alignment program for amino acid or nucleotide sequences
maker:Maker - Genome Annotation Pipeline
maple:Maple - Symbolic Algebra and Modeling Tool
maq:Maq - Mapping and Assembly with Qualities
masurca:MaSuRCA - whole genome assembly software
mathematica:Mathematica - Technical Computing Software
matlab:MATLAB - The Language Of Technical Computing
mcl:MCL - Markov Cluster Algorithm for Graphs
megahit:MEGAHIT -
meme:MEME - Motif-based Sequence Analysis Tools
mercurial:Mercurial - a free, distributed source control management tool
merdeep2:miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.
merdeep2:need load the following modules: squid/1.9g randfold/2.0 bowtie/0.12.8 viennarna/1.8.5 merdeep2/
meren-utils:meren-utils - collection of scripts to work with Illumina paired-end data
metamap:metamap - A Tool For Recognizing UMLS Concepts in Text
metaphlan2:MetaPhlAn v2.0: Metagenomic Phylogenetic Analysis
metaphyler:MetaPhyler - Estimating Bacterial Composition from Metagenomic Sequences
metavelvet:MetaVelvet: a short read assember for metagenomics
metaxa2:Metaxa2 - Improved Identification and Classification of SSU sequences in Environmental Datasets
metis:METIS - Serial Graph Partitioning and Fill-reducing Matrix Ordering
mip-scaffolder:MIP Scaffolder - Fast Scaffolding with Small Independent Mixed Integer Programs
mira:MIRA - sequence assembler for whole genome and EST / RNAseq data
mirdeep_star:MiRDeep*: An Integrated Application Tool For MiRNA Identification From RNA Sequencing Data
mirexpress:mirexpress - Analyzing high-throughput sequencing data for profiling microRNA expression
mne:MNE - MEG and EEG Preprocessing Tools
modelsim:ModelSim SE
Molpro:Molpro 2012.1.13 using Intel compilers and mvapich2/2.0rc-intel
mosaik:Mosaik - reference-guided aligner
mosek:Mosek Optmizer
mothur:mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
mpack:mpack - Multiple precision arithmetic BLAS (MBLAS) and LAPACK (MLAPACK)
mpfi:MPFI - Multiple Precision Interval Arithmetic Library
mpfr:MPFR - Floating Point Math Library
mpich:mpich - High-Performance Portable MPI
mplayer:Mplayer - multimedia player
mrbayes:MrBayes - Bayesian Inference of Phylogeny
MRIConvert:MRIConvert - a medical image file conversion utility
mricro:MRIcro - medical image viewer
mricrogl:MRIcroGL - medical image viewer
mricron:mricron - mricro utilties
mugsy:Mugsy - multiple whole genome alignment tool
multidistribute:Multidistribute - Rates of Molecular Evolution
multiz-tba:Multiz/TBA - local multiple sequence alignment tool
multovl:MULTOVL Multiple overlaps of genomic regions
mummer:MUMmer - Ultra-fast alignment of large-scale DNA and protein sequences
mumps:MUMPS - Multifrontal Massively Parallel Sparse Direct Solver
muscle:MUSCLE - Multiple Sequence Alignment
mvapich2:The MVAPICH2 Message Passing Library
mvapich2-gdr:The MVAPICH2 Message Passing Library + GPUDirect support
myrna:Cloud-scale differential gene expression for RNA-seq
nag-fortran-lib:NAG Fortran Library - The largest collection of reliable and supported numerical algorithms commercially available
nano:nano - text editor
nanocorr:nanocorr - Error correction for oxford nanopore reads
nasa-asp:NASA Ames Stereo Pipeline - Automated Geodesy & Stereogrammetry Tools
ncbi-toolkit:NCBI C++ Toolkit
ncl:NCL - NCAR Command Language
nco:NCO - netCDF Operators
ncview:ncview - Visual browser for netCDF files
netcdf:The Network Common Data Form
neuron:Neuron - for empirically based simulations of neurons and networks of neurons
nextclip:Nextclip = read preparation of data sequenced from Nextera LMP libraries
novoalign:NovoAlign - short read mapper
nvidia-driver:nvidia-driver - NVIDIA GPU Driver Libraries
nwchem:NWChem - High-Performance Computational Chemistry
openblas:Optimized BLAS Library Based on GotoBLAS2
openbugs:OpenBUGS - Bayesian Inference Using Gibbs Sampling
opencollada:OpenCollada Tools
opencv:OpenCV - Open Source Computer Vision Library
openexr:openexr - a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications
openmpi:The OpenMPI Message Passing Library
opera:Opera - Optimal Paired-End Read Assembler
ovito:ovito - Open Visualization Tool
p4est:p4est - Parallel AMR on Forests of Octrees
pagit:PAGIT - Post Assembly Genome Improvement Toolkit
paml:PAML - Phylogenetic Analysis by Maximum Likelihood
pandaseq:align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence
papi:PAPI - Performance Application Programming Interface
paraview:ParaView - Data Analysis and Visualization
parmetis:ParMETIS - Parallel Graph Partitioning
pastix:PaStiX Parallel Sparse matriX package
patser:Patser find locations of patterns in sequence
pauda:PAUDA - a high-throughput metagenomic protein database search tool
pbalign:for aligning PacBio reads to reference sequences
pbh5tools:pbdh5tools - is a collection of tools that can manipulate the content or extract data from two types of h5 files.
pbjelly:PBJelly - Genome Upgrading using Long-Read Sequencing
pbsuite:PBSuite - Software for Long-Read Sequencing Data from PacBio
pdftk:pdftk - pdf toolkit
pdsh:pdsh - Parallel Distributed Shell
pe-assembler:PE-Assembler - De novo assembler using short paired-end reads
penncnv:PennCNV - CNV detection from Illumina whole-genome SNP genotyping arrays
perl:The Perl Programming Language
petsc:PETSc - Portable, Extensible Toolkit for Scientific Computation
pgi:PGI - Portland Group Compiler Suite
phrap:Phrap/Phred/Consed - genome assembler
phylip:Phylip - package for inferring phylogenies
phylobayes:Bayesian Monte Carlo Markov Chain sampler for phylogenetic reconstruction
phyml:PhyML is a phylogeny software based on the maximum-likelihood principle.
phymmbl: Taxonomic Classification of Metagenomic Short Reads
phyutility:Phyutility (fyoo-til-i-te) is a command line program that performs simple analyses or modifications on both trees and data matrices.
picard-tools:Java-based command-line utilities that manipulate SAM file
pigz:pigz - parallel implementation of gzip
pindel:pindel - genome data analizer
plink:Plink - Whole genome data analysis toolset
polyphen:PolyPhen - Polymorphism Phenotyping
pov-ray:Persistence of Vision Ray Tracer
price:PRICE - Paired-Read Iterative Contig Extension
proovread:large-scale high-accuracy PacBio correction through iterative short read consensus
prot4est:prot4EST - perl script to translate ESTs to putative peptides
pyferret:Ferret Data Visualization and Analysis (Python encapsulation)
pymol:PyMOL - A Python-enhanced molecular graphics tool
pypy:PyPy - Fast, Alternative Implementation of Python
python:The Python Programming Language
qiime:QIIME - Quantitative Insights Into Microbial Ecology
qt:Qt - Cross-Platform Application and UI Framework
quake:Quake - Correct Substitution Sequencing Errors
quantumespresso:Quantum Espresso - electronic-structure calculations and materials modeling at the nanoscale
quip:QUIP - The QUIP package (GitHub) is a collection of software tools to carry out molecular dynamics simulations.
quiver:PacBio variant and consensus caller (Quiver algorithm)
R:The R Project for Statistical Computing
randfold:Randfold compute the probability that, for a given RNA sequence, the Minimum Free Energy (MFE) of the secondary structure is different from a distribution of MFE computed with random sequences.
raxml:RAxML - Randomized Accelerated Maximum Likelihood
readscan:READSCAN - a highly scalable parallel program to identify non-host sequences and estimate their genome relative abundance in high-throughput sequence datasets
reapr:REAPR - Recognising Errors in Assemblies using Paired Reads
recon:RECON - a package for automated de novo identification of repeat families from genomic sequences
repeatmasker:RepeatMasker - Screens DNA Sequences for Interspersed Repeats
repeatmodeler:RepeatModeler is a de-novo repeat family identification and modeling package.
repeatscout:RepeatScout - The purpose of the RepeatScout software is to identify repeat family sequences from genomes where hand-curated repeat databases
reptile:Reptile - Short Read Error Correction
retroseq:RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements.
rex:Region of Interest mapping
rmblaster: RMBlast is a RepeatMasker compatible version of the standard NCBI BLAS 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.
rmc++:RMC++ - Reverse Monte Carlo Algorithm
rnashapes:rnashapes - RNA shape mapping
root:Root - A Data Analysis Framework
rosetta:Rosetta - algorithms for computational modeling and analysis of protein structures
rsem:RSEM - RNA-Seq by Expectation-Maximization
rseqc:RSeQC - An RNA-seq Quality Control Package
rstudio:RStudio - Integrated Development Environment (IDE) for R
rtd:rtd - reference-free ddRADseq analysis tools
ruby:The Ruby Programming Language
sage:Sage is a free open-source mathematics software system
salmon:Salmon - Rapid Alignment-free Quantification of Isoform Abundance
samtools:SAMtools - Sequence Alignment/Map Format
SAS:SAS statistical Analysis
scala:Scala is a general purpose programming language designed to express common programming patterns in a concise, elegant, and type-safe way.
scarpa:SCARPA - stand-alone scaffolding tool for NGS data
scons:Scons - python based build environment
scotch:SCOTCH - Software and libraries for sequential and parallel graph partitioning, static mapping and clustering, sequential mesh and hypergraph partitioning, and sequential and parallel sparse matrix block ordering
seg3d:Seg3D volume segmentation and processing tool
selscan:Selscan - calculates EHH-based scans for positive selection in genomes
seqdb:SeqDB - High-throughput compressor for FASTQ files
seqtk:Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format
sextractor:Source Extractor: a software for making catalog of sources from astronomical images
sextractor:sextractor.xsl is in %(rootdir)s/share
sga:SGA - String Graph Assembler
shogun:Shogun - A Large Scale Machine Learning Toolbox
shrimp:SHRiMP - sensitive yet practical SHort Read Mapping
siesta:SIESTA - electronic structure calculations and molecular dynamics simulations
slatec:slatec - a comprehensive software library containing over 1400 general purpose mathematical and statistical routines written in Fortran 77.
slepc:SLEPc, the Scalable Library for Eigenvalue Problem Computations
slim:SLiM (Selection on Linked Mutations) is a forward population genetic simulation for studying linkage effects
slurm-drmaa:an implementation of Open Grid Forum DRMAA 1.0 (Distributed Resource Management Application API) specification for submission and control of jobs to SLURM.
smrtanalysis:SMRT Analysis - PacBio bioinformatics software suite
SNAP-berkeley:Scalable Nucleotide Alignment Program
snap-ucdavis:Semi-HMM-based Nucleic Acid Parser
snpeff:SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).
soapdenovo2:SOAPdenovo2 - De Novo Draft Assembly for Human-Sized Genomes
spades:SPAdes - St. Petersburg genome assembler
sparsehash:sparsehash - extremely memory-efficient hash_map implementation
spimap:SPIMAP - Species Informed Maximum A Posteriori Gene Tree Reconstruction
spm:Statistical Parametric Mapping
sqlite:SQLite - embedded SQL database engine
squid:SQUID - C functions and utility programs for sequence analysis
sratoolkit:SRA Toolkit - NCBI Sequence Read Archive
stampy:Stampy - sensitive and fast mapping of Illumina sequence reads
star:STAR - ultrafast universal RNA-seq aligner
star-fusion:STAR-Fusion -
stata:STATA - Data Analysis and Statistical Software
sublime:sublime - Chemical Kinetics and Dynamics Tools
suitesparse:SuiteSparse - Sparse Matrix Packages
surpi:SURPI - computational pipeline for pathogen identification
svdetect:svdetect - a tool to detect genomic structural variations from paired-end and mate-pair sequencing data
svn:Subversion - Enterprise-class centralized version control for the masses
swarm:The purpose of swarm is to provide a novel clustering algorithm that handles massive sets of amplicons.
swig: interface compiler that connects programs written in C and C++ with scripting languages
swipe:SWIPE - Smith-Waterman with inter-sequence SIMD parallelisation
synopsys:Synopsys - electronic design software (Licensed by Engineering)
tabix:Tabix - Indexer for TAB-delimited genome position files
talys:Talys - Nuclear reaction simulation
tangram:tangram - structural variation detection
tao:TAO Toolkit for Advanced Optimization
tea:Tea - transposable element analysis pipeline
tecplot:Tecplot 360/Focus - Visualization and Plot Software
tesseract:tesseract - Open Source OCR Engine
texlive:Texlive - resource to create TeX files
tlex:T-lex - a computational pipeline that detects presence and/or absence of annotated individual transposable elements (TEs) using next-generation sequencing (NGS) data
tophat:TopHat - fast splice junction mapper for RNA-Seq reads
totalview:Totalview from Rougue Wave
trackvis:analysis of fiber track data from diffusion MRI tractography
tramonto:Tramonto for Nanostructured Fluids in Materials and Biology
trans-abyss:Analyze ABySS multi-k-assembled shotgun transcriptome data.
trans-abyss:need load: bwa samtools abyss gmap-gsnap
transdecoder:TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
transrate:Transrate is software for de-novo transcriptome assembly quality analysis.It examines your assembly in detail and compares it
to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies
treeview:Java Treeview - An Open Source, Extensible Viewer for Microarray Data in the PCL or CDT format.
trilinos:Trilinos - Algorithms for Engineering and Scientific Problems
trimgalore:Trim Galore - wrapper script to automate quality and adapter trimming
trimmomatic:Trimmomatic - read trimming tool for Illumnia NGS data
trinity:Trinity - RNA-Seq De Novo Assembly
trinotate:Trinotate - Transcriptome Functional Annotation and Analysis
turbovnc:TurboVNC - High Performance Virtual Network Computing
uclust:UCLUST offers search and clustering algorithms that are often orders of magnitude faster than BLAST
udunits:UDUNITS - Library for handling of units of physical quantities
usearch:USEARCH - Extreme high-throughput sequence analysis
valgrind:Valgrind - Debugging and Profiling System
vasp:VASP - Vienna Ab-initio Simulation Package
vcftools:vcftools - a program package designed for working with VCF files
velvet:Velvet - Sequence Assembler for Very Short Reads
verilator:Verilator is the fastest free Verilog HDL simulator, and beats most commercial simulators.
viennarna:RNA Secondary Structure Prediction and Comparison
visit:VisIt - Parallel Visualization and Analysis Package
vmd:Visual Molecular Dynamics
vnc-apps:vnc-apps - helpful X tools for vnc sessions
voro++:Voro++ - library for the computation of the Voronoi diagram
votca:votca - molecular dynamics code
vpython:vpython - experimental python based on wxpython
vrpn:VRPN - Virtual Reality Peripheral Network
vsfm:VisualSFM: A Visual Structure from Motion System
vtk:VTK - The Visualization Toolkit
vxl:VXL C++ Libraries for Computer Vision Research and Implementation
wcstools:create, display and manipulate the world coordinate system of a FITS or IRAF image
weblogo:WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible
wgs:Celera Assembler (CA) is a whole-genome shotgun (WGS) assembler for the reconstruction of genomic DNA sequence from WGS sequencing data.
wise2:wise2 - a program for aligning proteins or protein HMMs to DNA
xcrysden: Xcrysden semishared binary v. 1.5.53
xhmm:XHMM - eXome-Hidden Markov Model
xsede:Globus Client for XSEDE
yasra: YASRA - Comparative Genome Assembler
zeromq:Zeromq Intelligent Transport Layer
zlib:zlib compresion library