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Software Overview

On the WestGrid systems there is a core of common software, but due to user requirements or limitations of licensing or architecture, there are some differences in the programs offered at the various WestGrid sites. The tables below and the associated database summarize the majority of the software that has been added to the basic Linux environment.  Not every package has an entry in this database. For example, software that is licensed only to a specialized group of researchers may not be listed. Also, add-on modules for R, Perl and Python are less likely to be listed.

If software you require is not included in the lists here, please contact us to see if it can be installed.

Once you have located software of interest, either by scrolling through the full listing or by using the Search button and associated pull-down menus to filter the software by category or system, click on the software title.  That will lead to a page showing the software versions available on WestGrid systems as well as usage instructions for some packages.

The executables for commonly used software can usually be found on the PATH supplied by the default login environment at each WestGrid site. Some of the software is configured with the module command. Additional software, libraries, including files, documentation and other supporting files sometimes do not fit readily into a rigid installation scheme, but are usually installed under one or two standard directories for each site, such as /global/software.

All WestGrid Software

Software Category: Bioinformatics / Genomics Applications
Software Brief Description
ADMIXTURE ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.
Annovar ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).
BamTools BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files.
bgc bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci.
BMTagger Best Match Tagger (BMTagger) is an efficient tool that discriminates between human reads and microbial reads without doing an alignment of all reads to the human genome.
CAP3 A DNA Sequence Assembly Program
CNVnator a tool for CNV discovery and genotyping from depth of read mapping.
DosageConverter DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther formats such as MaCH or PLINK.
ESTScan ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality.
FastTree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
FStitch This software is written primarily for scientists looking to identify putative nascent transcripts de novo in Global Run-On sequencing.
GOTTCHA GOTTCHA (Genomic Origin Through Taxonomic CHAllenge) is an application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly smaller false discovery rates (FDR) that is also laptop deployable.
hisat2 graph-based alignment of next generation sequencing reads to a population of genomes
Homer HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis.
HTSlib A C library for reading/writing high-throughput sequencing data
IDBA-UD IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data
Image Iterative Mapping and Assembly for Gap Elimination
Kraken Kraken is a Taxonomic Sequence Classification System
Mach MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.
MEGAHIT An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
Megan Stand-alone analysis tool for metagenomic of short-read data
MetaVelvet MetaVelvet identifies shared nodes (named chimeric nodes) between two subgraphs and disconnects two subgraphs by splitting the shared nodes.
Minimac2 minimac2 is an improved version of Minimac.
Minimac3 Minimac3 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and minimac2.
PEAR PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.
PHAST (Phylogenic Analysis with Space/Time Models) PHAST (Phylogenic Analysis with Space/Time Models)
PRINSEQ PReprocessing and INformation of SEQuence data
Relion RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM).
RNAmmer RNAmmer predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.
SCUBAT SCUBAT (Scaffolding Contigs Using BLAT And Transcripts) uses any set of transcripts to identify cases where a transcript is split over multiple genome fragments and attempts to use this information to scaffold the genome.
SHRiMP SHRiMP - SHort Read Mapping Package
SignalP SignalP 4.1 predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms
smalt SMALT aligns DNA sequencing reads with a reference genome.
SVDetect A tool to identify genomic structural variations from paired-end and mate-pair sequencing data
TMHMM Prediction of transmembrane helices in proteins
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.
Trimmomatic A flexible read trimming tool for Illumina NGS data
VarSim A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications.
WebLogo WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.
ABySS Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. See also Trans-ABySS below.
ALLPATHS-LG Sequence assembly program.
ARB Sequence database handling and phylogenic analysis.
Augustus AUGUSTUS is a gene prediction program for eukaryotes.
BCFtools (VCF/BCF file manipulation) BCFtools is a set of utilities for manipulating Variant Call Format and related files.
bcl2fastq - Illumina BCL to FASTQ conversion utility bcl2fastq - Illumina BCL to FASTQ conversion utility
BEAGLE (beagle-lib) Broad-platform Evolutionary Analysis General Likelihood Evaluator - library for speeding up phylogenetic calculations.
BEAST BEAST (Bayesian Evolutionary Analysis by Sampling Trees).
BEDTools Utility suite for comparing genomic features.
biobambam biobambam - a set of tools for processing BAM format sequence files.
BioPerl Collection of Perl-based tools for bioinformatics.
Biopython Collection of Python-based tools for bioinformatics.
BLAST A suite of tools for assessing the similarity of a given sequence of proteins or nucleotides with a database of sequences.
BLAT BLAST-Like Alignment Tool. See the BLAT site for more information.
Bowtie Short read DNA sequence aligner.
Bowtie2 Short read DNA sequence aligner.
BUCKy (phylogenetic analysis) BUCKy - Bayesian phylogenetic analysis of gene tree concordance.
BWA Burrows-Wheeler Aligner - Aligns short nucleotide sequences to long reference sequences.
Cd-hit CD-HIT is a program for clustering DNA/protein sequence database at high identity with tolerance.
Celera Whole-Genome Shotgun Assembler Celera whole-genome shotgun sequence assembler and conversion utilities.
Censor Censor compares and masks protein or nucleotide sequences.
Clustal Omega Clustal Omega - Multiple protein sequence alignment
Coral Error correction software for DNA sequence analysis.
Cufflinks Transcript assembly from RNA-Seq data.
DIAMOND - sequence aligner Program for local aligments of translated nucleotide or amino acid sequences to protein references
DISCOVAR and DISCOVAR de novo - genome assembly DISCOVAR de novo whole genome shotgun assembler from 250-base Illumina PCR-free fragment reads.
ExaML/RAxML - Phylogenetic tree analysis Phylogenetic tree analysis.
Exonerate exonerate is a generic tool for pairwise sequence comparison.
FastQC Quality control tool for high throughput sequence data.
fastStructure (population genetics) Infer population structure from large SNP genotype data.
FASTX-Toolkit (sequence pre-processing) FASTX-Toolkit - command line tools for short read sequence data pre-processing.
GATK "The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data."
GMAP (with GSNAP) - Genomic mapping and alignment GMAP (with GSNAP) - Genomic mapping and alignment package.
HMMER Homolog search and protein sequence alignments.
IMa2 Isolation and migration effects in population genetics.
IMPUTE (genotype imputation) IMPUTE2 - Version 2 of IMPUTE for genotype imputation and haplotype phasing
IQ-TREE (phylogenetics) IQ-TREE is a phylogenetics package for inferring maximum likelihood trees.
JELLYFISH DNA substring (k-mer) counting.
kSNP3 - find SNPs in DNA sequences and estimate phylogenetic trees kSNP3 - Software to find single nucleotide polymorphisms in DNA sequences and estimate phylogenetic trees
Maker MAKER is a portable and easily configurable genome annotation pipeline.
MaSuRCA - whole genome assembler MaSuRCA whole genome assembler
MEME Suite Identify motifs (patterns) in sequences.
MetAMOS MetAMOS - framework for genome assembly and analysis.
MetaVelvet An extension of Velvet assembler to de novo metagenome assembly from short sequence reads.
Migrate (Migrate-n) - Population genetics program to estimate migration rates and population sizes Migrate-n is a population genetics program for estimating migration rates and population sizes.
Mothur Bioinformatics software for microbial ecology.
MrBayes Bayesian inference for phylogenetic and evolutionary models.
MUMmer Alignment of large DNA and protein sequences.
Muscle multiple alignment program
Nemo Stochastic simulation to study evolution of life history/phenotypic traits and population genetics.
Pandaseq To align Illumina reads and reconstruct an overlapping sequence
Picard tools Java-based tools for manipulation of BAM (Binary sequence alignment map) data files.
PLINK Analysis of genotype/phenotype data.
Prodigal Prodigal: Prokaryotic Dynamic Programming Genefinding Algorithm
QIIME Quantitative Insights into Microbial Ecology.
RAPSearch (protein similarity search) RAPSearch/RapSearch2 - Reduced Alphabet-based Protein similarity Search
Ray De novo genome assembly.
RepeatMasker RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
RITA Rapid Identification of Taxonomic Assignments. Nucleotide sequence analysis.
RMBlast RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite.
RSEM Package for estimating gene and isoform expression levels from RNA-Seq data.
SAMtools and HTSlib utilities SAMtools is a set of utilities for manipulating SAM (Sequence Alignment/Map) format files.
SGA Memory efficient de novo assembler of high-coverage short-read sequence data for large genomes
SHAPEIT (estimation of haplotypes) SHAPEIT - Halotype estimation (phasing) from genotype or sequencing data
SNAP (Semi-HMM-based Nucleic Acid Parser) gene prediction tool.
SNPTEST SNPTEST - Program for whole-genome SNP association studies
SOAPdenovo Short Oligonucleotide Analysis Package for Illumina GA short-read assembly.
SOAPdenovo-Trans SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.
SPAdes Genome Assembler SPAdes - assembler for bacterial genomes
Stacks Software pipeline for analysis of short-read genetic sequences for application to population genomics
STAR STAR: Spliced Transcripts Alignment to a Reference
Tablet - Next Generation Sequence Assembly Visualization Tablet is a graphical viewer for next generation sequence assemblies and alignments.
Tandem Repeats Finder Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
TopHat Exon splice junction mapper based on BowTie RNA-Seq alignments.
TPP The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.
Trans-ABySS A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.
Treemix TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.
Trinity De novo reconstruction of transcriptomes from RNA-seq data.
Trinotate Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.
VCFtools a program package designed for working with VCF files
Velvet Package for genomic sequence assembly from short-read data.
WHAM/WHAMG - WHole-genome Alignment Metrics WHAM/WHAMG - WHole-genome Alignment Metrics for structural variant detection and association testing
Software Category: Chemistry and Biochemistry Applications
Software Brief Description
ATSAS A program suite for small-angle scattering data analysis from biological macromolecules
AutoDock_vina AutoDock Vina is an open-source program for doing molecular docking.
dl_meso The DL_MESO Mesoscale Simulation Package
GROMACS A molecular dynamics program (along with attendant utilities) designed for simulations of large molecules, such as proteins.
Memprot Memprot is a program that aims to fit Small Angle X-ray Scattering curves of detergent solubilized membrane proteins.
openkim The KIM API is an Application Programming Interface for atomistic simulations.
PLUMED PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines.
ShengBTE - solving Boltzmann Transport Equation for phonons ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons.
Smoldyn Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution.
Spglib Spglib is a C library for finding and handling crystal symmetries.
ABINIT Electronic structure calculations, based on Density Functional Theory, for the treatment of molecules and periodic solids.
Adaptive Poisson-Boltzmann Solver (APBS) Software for modelling biomolecular solvation.
Amber A suite of programs for molecular calculations, including molecular dynamics.
ASE ASE is an Atomistic Simulation Environment written in the Python
AutoDock A suite of programs for predicting how small molecules will bind to a target of known 3D structure.
BigDFT A massively-parallel wavelet-based DFT code for solid state/nanoclusters modeling for material science.
Cantera Cantera is an object-oriented software toolkit for chemical kinetics, thermodynamics, and transport processes
Chaste Cancer, Heart and Soft Tissue Environment - tissue and cell level electro-physiology, discrete and soft tissue modelling.
CP2K Software for ab initio molecular dynamics based on mixed plane waves and Gaussian basis sets.
CPMD Software for ab initio molecular dynamics. Users should be aware of the license requirements.
Dalton Together, the two programs, Dalton and LSDalton, provide an extensive functionality for the calculations of molecular properties at the HF, DFT, MCSCF, and CC levels of theory. Many of these properties are only available in the Dalton2016 suite.
DFTB+ - Density Functional based Tight Binding (DFTB) method with extensions DFTB+ - Package implementing the Density Functional based Tight Binding (DFTB) method with extensions
DIRAC Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations.
DL_POLY DL_POLY is a suite of programs developed at Daresbury Laboratory for molecular dynamics simulations of a variety of systems, including "macromolecules, polymers, ionic systems and solutions".
Elk An electronic structure code for determining the properties of crystalline solids.
EXCITING A full-potential all-electron DFT package based on the linearized augmented plane-wave (LAPW) method.
GAMESS A general molecular ab initio quantum chemistry package
Gar2ped a Gaussian 94 output postprocessing utility
Gaussian A suite of programs for semi-empirical and ab initio molecular orbital calculations.
Gulp GULP is a program for performing a variety of types of simulation on materials
HOOMD-blue particle simulation toolbox HOOMD-blue - General purpose particle simulation toolkit.
LAMMPS LAMMPS, Large-scale Atomic/Molecular Massively Parallel Simulator
MGLTools including AutoDockTools MGLTools, including AutoDockTools (ADT) is a suite of programs for molecular structure visualization and analysis.
Molden A visualization, pre- and post-processing program for molecular and electronic structure.
MOPAC MOPAC (Molecular Orbital PACkage) is a general-purpose semiempirical quantum chemistry package for the study of solid state and molecular structures and reactions.
NAMD A molecular dynamics simulator for large biomolecular systems.
NBO NBO: Natural Bond Orbital analysys program
NEURON An environment for simulating neurons and networks of neurons.
NWChem Scalable open-source solution for large scale molecular simulations.
Open Babel Data conversion toolkit.
OpenMX Open Materials Explorer - O(N) massively parallel DFT code for nano-scale material science.
ORCA An ab initio, DFT and semiempirical SCF-MO package.
PDB2PQR Preparing structures for continuum electrostatics calculations.
Phonopy Phonopy is an open source package of phonon calculations based on the supercell approach.
Priroda Priroda is a fast parallel relativistic DFT/ab initio code for molecular modeling
PSI PSI is an open-source suite of ab initio quantum chemistry programs
Qbox DFT Based electronic structure and molecular dynamics program.
Quantum ESPRESSO A suite of programs for electronic structure and materials modelling.
QWalk QWalk is an efficient Quantum Monte Carlo code by the group of Lucas Wagner
Rosetta Software Suite Protein design and analysis. Write to WestGrid support for access information.
SIESTA An electronic structure (periodic, linear scaling DFT) code and molecular dynamics package.
Sire Sire is a free, open source, multiscale molecular simulation framework, written to allow computational modelers to quickly prototype and develop new algorithms for molecular simulation and molecular design.
VASP An ab-initio quantum-mechanical molecular dynamics package based on pseudopotentials and a plane wave basis set.
WebMO WebMO is a web portal for running and visualization of Computational Chemistry computations
XCrySDen XCrySDen is a crystalline and molecular structure visualisation program
YAeHMOP Yet Another extended Huckel Molecular Orbital Package.
Yambo Ab initio code for quasi-particle excited state energies and optical properties for solid state and molecular physics applications.
Software Category: Graphics
Software Brief Description
Avizo GUI-based application for scientific data visualization and analysis
Gephi - interactive network graph visualization Gephi - an interactive program for network graph visualization
Circos Oriented towards genomic data display but can be applied to other data.
Eye of GNOME Image viewer (eog).
Ezys - GPU-accelerated non-rigid 3D medical image registration Ezys - GPU-accelerated non-rigid 3D medical image registration
FFmpeg (video encoding) FFmpeg - create a movie file from a series of images
Gbrowse GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.
GDIS GDIS is a scientific visualization program for the display, manipulation, and analysis of molecular and periodic structures.
GLUT A toolkit that implements a simple windowing application programming interface (API) for OpenGL.
GMT - Generic Mapping Tools A script-driven package of utilities for gridding and contouring geographic and Cartesian data sets, with support for many map projections.
Gnuplot Command-driven x-y plotting program, generally of lower quality than xmgrace, but offering some 3D features.
Grace/Xmgrace GUI-based x-y plotting for thesis and publication-quality graphs.
ImageMagick Software suite for image format conversion and editing.
libjpeg Independent JPEG Group JPEG compression library and image file conversion programs, djpeg and cjpeg.
libpng Library for handling PNG raster images.
libtiff TIFF (Tagged Image File Format) image library.
links View HTML files or URL
Luscus Luscus is a program for graphical display and editing of molecular systems.
Matplotlib Python-based 2D (mostly) plotting library.
mencoder (MPEG encoding) mplayer (video player).
Mesa Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
MINC - Toolkit Medical Imaging NetCDF (MINC) Toolkit
Molekel Molekel is an open-source multi-platform molecular visualization program
NCAR Graphics and NCL Libraries and utilities for contour maps, vector and streamline plots, X-Y graphs, map databases, etc.
Ncview Visual browser for NetCDF files.
Netpbm Image conversion utilities and library.
ParaView GUI-based application for visualization of many types of multi-dimensional data.
pdflib PDF file handling library ("PDFlib-Lite" for non-commercial use).
PLplot PLplot is a cross-platform software package for creating scientific plots.
PyMOL - Molecular visualization system PyMOL - Molecular visualization system
Qt Application and user interface development framework.
Rasmol Molecular graphics visualization.
Vendor's OpenGL
VISAT An image processing and data analysis program for remotely sensed data.
VisIT - general purpose visualization tool VisIT - general purpose scientific visualization tool
VMD VMD is a program for displaying and animating large biomolecular systems.
VTK - Visualization Toolkit Comprehensive libraries for visualization of many types of multi-dimensional data.
wkhtmltox Convert HTML to PDF and various image formats
xv Image display and manipulation utility
zlib Data compression library.
Software Category: Other Applications
Software Brief Description
CISM The Community Ice Sheet Model (CISM) is a next-generation ice sheet model used for predicting ice sheet evolution and sea level rise in a changing climate.
CLHEP A Class Library for High Energy Physics
CompuCell3D CompuCell3D is an open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms.
GATE GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to numerical simulations in medical imaging and radiotherapy.
Geant4 Geant4 is a toolkit for the simulation of the passage of particles through matter.
ABAQUS Comprehensive finite element modelling package
ANSYS simulation software, including Fluent and CFX ANSYS simulation software, including computational fluid dynamics packages Fluent and CFX
BEAM A toolbox for viewing and analyzing remotely-sensed data.
Gadget Simulation of cosmological structure formation.
GDAL Geospatial Data Abstraction Library.
GRIB-API GRIB-API is an API for working with GRIB meteorological data format.
libLAS ASPRS LiDAR data translation tools.
Lumerical FDTD Solutions Lumerical FDTD Solutions empowers designers to confront the most challenging photonic design problems.
MATLAB A general purpose numerical package with a high-level programming language for linear algebra, signal processing, image processing, 2-D and 3-D graphics, etc.
MEEP Finite difference time-domain (FDTD) electromagnetic simulation package.
MOM The Modular Ocean Model (MOM) is a numerical ocean model based on the hydrostatic primitive equations.
MuMax3 - Micromagnetic Simulation MuMax3 - micromagnetic simulator
Octave A general purpose numerical package that is largely compatible with MATLAB.
OpenFOAM, OpenFOAM+ and OpenFOAM Extend Toolkit for building CFD applications.
OpenSees Open System for Earthquake Engineering Simulation
PROJ.4 Cartographic Projections library
Seismic Un*x An open source collection of software for seismic processing and research.
Seplib A seismic data processing package from the Stanford Exploration Project (SEP).
WRF Weather Research & Forecasting Model, including WPS (WRF Pre-processing system), WRF-Chem and WRF EMS (Environmental Modeling System).
Software Category: Files and Data
Software Brief Description
Hadoop Tool for map/reduce-style calculations
parallel-netcdf A Parallel I/O Library for NetCDF File Access
Climate Data Operators (CDO) A command line suite for manipulating and analysing climate data.
Emacs GNU version of this common text editor.
gedit - graphical text editor gedit - graphical text editor with syntax highlighting
HDF 4 Hierarchical Data Format is a file format for scientific data of various kinds, including both floating point and raster image types.
HDF 5 Hierarchical Data Format - file format for storing a variety of data types.
jEdit A graphical editor for programmers (requires X Windows).
nano A simple non-graphical text editor with on-screen reminders for commonly-used commands (similar to pico).
NCO A set of programs for manipulating data in NetCDF files.
NEdit A graphical editor recommended for PC users, but requires X Windows.
NetCDF A set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
Szip A library for lossless compression of scientific data.
TecIO A library for writing data for import into Tecplot.
Vim An enhanced version of the vi text editor.
Software Category: Programming
Software Brief Description
Swig SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
Allinea DDT Powerful commercial debugger/profiler/Analyzer with useful GUI.
Blitz++ C++ template library for dense vectors and multi-dimensional arrays.
Boost An eclectic collection of C++ libraries.
CLAPACK F2C translation of LAPACK
CMake Cross platform software build system
Compilers - C, C++ and Fortran Compilers - C (gcc, icc, pgcc), C++ (g++, icpc, pgCC), Fortran (gfortran, ifort, pgf77, pgf90, pgf95)
dbx Common UNIX debugger.
ddd Graphical front end to other debuggers.
Eigen C++ template library for linear algebra.
Expat Expat is an XML parser library written in C.
gdb GNU debugger.
Git Version control system.
GNU Data Language (GDL) A tool for data analysis and visualization in such disciplines as astronomy, geosciences and medical imaging.
GNU libgomp GNU implementation of the OpenMP Application Programming Interface (API).
Go The Google Go programming language
idb Intel debugger.
Jam Make replacement for C/C++ projects.
Java Java is a programming language and computing platform.
Julia Julia is a high-level, dynamic language for technical computing
LibYAML LibYAML is a YAML 1.1 parser and emitter written in C.
LIKWID - Performance analysis tools LIKWID - Performance analysis tools for OpenMP and hybrid OpenMP/MPI programs.
Lua Lua is a powerful, fast, lightweight, embeddable scripting language.
Mercurial Distributed version control system
Mono (C# environment) Mono .NET environment to provide a platform for running C# programs.
Node.JS Node.JS asynchronous, event driven, standalone JavaScript language implementation.
OCaml OCaml: industrial strength programming language supporting functional, imperative and object-oriented styles
Perl Perl is a family of high-level, general-purpose, interpreted, dynamic programming languages.
pgdbg Portland Group graphical debugger.
Python Python is an interactive, object-oriented, extensible programming language.
ROOT (data analysis framework) ROOT is an object-oriented framework aimed at solving the data analysis challenges of high-energy physics.
RStudio Integrated Development Environment for R
Ruby A dynamic, interpreted, open source programming language with a focus on simplicity and productivity.
SCons SCons is an Open Source software construction tool
STLport An implementation of the Standard Template Library.
Subversion An open source alternative to CVS for managing files for large development projects.
tvmet Tiny Vector Matrix library using Expression Templates.
Xerces-C++ XML parser and writer.
zzFormatTest Create/Edit/Format test, please ignore
Software Category: Database management and tools
Software Brief Description
MySQL MySQL is a popular open source database
PostgreSQL PostgreSQL is a powerful, open source object-relational database system.
Software Category: Mathematical Libraries and Applications
Software Brief Description
AlmaBTE A Solver of the Space- and Time-Dependent Boltzmann Transport Equation for phonons.
BLAS Basic Linear Algebra Subprograms.
CGAL A C++ library for geometric algorithms.
deal.II Library for partial differential equation solution with adaptive finite elements.
FEniCS A framework for solution of differential equations by finite element methods. DOLFIN is a key component of the FEniCS environment.
FETK FETK: The Finite Element ToolKit for solving differential equations.
FFTW A widely-used FFT implementation.
FreeFem++ - Partial Differential Equation Solver FreeFem++ is typically applied to solve multiphysics non-linear systems.
Gerris Flow Solver Gerris Flow Solver - solve partial differential equations for incompressible flow
GHMM The General Hidden Markov Model library (GHMM) is a freely available C library implementing efficient data structures and algorithms for basic and extended HMMs with discrete and continous emissions.
GSL A numerical library for C and C++ programmers including numerical integration, linear algebra, minimization, special functions and other mathematical routines.
Ipopt Interior Point OPTimizer for large-scale nonlinear optimization.
JAGS Just Another Gibbs Sampler - analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.
LAPACK Linear algebra subroutine package.
Maple Mathematical computation engine
Mathematica A comprehensive system for mathematical calculations.
MATLAB Compiler Runtime (MCR) The MATLAB Compiler Runtime (MCR) is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.
METIS Mesh and graph partitioning.
MKL MKL is a vendor optimized numerical library with C and Fortran bindings for BLAS, LAPACK, ScaLAPACK, FFT, a sparse system solver, random number generators and vector versions of common mathematical functions.
MMG3D Anisotropic tetrahedral remesher/moving mesh generation.
MPFR The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
MUMPS Parallel direct solver for sparse systems.
muParser muParser is an extensible high performance math expression parser library written in C++.
Nektar++ Framework for partial differential equation solvers based on finite-element methods.
NetworkX A Python-based package for creating and analyzing graphs (networks of nodes and edges).
NLopt Nonlinear optimization library.
OpenBUGS Bayesian inference Using Gibbs Sampling using Markov Chain Monte Carlo (MCMC) simulation.
p4est Parallel adaptive mesh refinement.
PARI/GP - computer algebra system PARI/GP - C library and interactive shell supporting calculations in number theory.
PETSc Toolkit for parallel solution of differential equations.
R Software environment and language for statistical data analysis.
SAS Statistical analysis software.
ScaLAPACK ScaLAPACK is a parallelized subset of the LAPACK linear algebra package.
scikit-learn Scikit-Learn a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering.
SCOTCH Graph and mesh partitioning, sparse matrix ordering.
SGI Solver - Fast Sparse Solvers SGISolve provides two direct solvers, PSLDLT and PSLDU, and one iterative solver, DIterative (deprecated), for sparse linear systems of equations.
SLEPc PETSc add-on eigenvalue solver for large sparse systems.
SuiteSparse a Suite of sparse matrix packages
SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers) SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers)
TetGen Tetrahedral mesh generation and 3D Delaunay triangulator.
Trilinos Object-oriented framework for linear algebra, meshing, preconditioners, solvers.
Software Category: UNIX Environment
Software Brief Description
64-bit Linux CentOS CentOS is an Enterprise-class Linux Distribution derived from sources freely provided to the public by a prominent North American Enterprise Linux vendor.
64-bit Red Hat Enterprise Linux A Linux-based operating system developed by Red Hat and targeted towards the commercial market.
64-bit Scientific Linux An operating system distributed by CERN that is similar to and compatible with CentOS.
64-bit SLES 11 A Linux-based operating system designed for servers, mainframes, and workstations.
bash (default) Bash is a Unix shell.
csh The improved version of tcsh.
Intel MPI A multi-fabric message passing library that implements the Message Passing Interface.
ksh It is an interactive command language that provides access to the UNIX system and to many other systems, on the many different computers and workstations on which it is implemented.
MVAPICH2 MVAPICH2 is an MPI implementation
Open MPI The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners.
Parallel GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
Red Hat Enterprise Linux AS A Linux-based operating system developed by Red Hat and targeted toward the commercial market.
tcsh It is a command language interpreter usable both as an interactive login shell and a shell script command processor.
zsh Zsh is a shell designed for interactive use, although it is also a powerful scripting language.