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Software Overview

National Systems

For information on software available on Compute Canada's national systems please refer to the Available Software page on the Compute Canada User Documentation wiki. 

WestGrid Systems

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.
CNVnator a tool for CNV discovery and genotyping from depth of read mapping.
DiScRIBinATE
DosageConverter DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther formats such as MaCH or PLINK.
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.
HTSlib A C library for reading/writing high-throughput sequencing data
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
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.
SignalP SignalP 4.1 predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms
Structure The program structure is a free software package for using multi-locus genotype data to investigate population structure.
Subread Subread package: high-performance read alignment, quantification and mutation discovery
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
ABySS Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. See also Trans-ABySS below.
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.
BEAGLE (beagle-lib) Broad-platform Evolutionary Analysis General Likelihood Evaluator - library for speeding up phylogenetic calculations.
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.
BWA Burrows-Wheeler Aligner - Aligns short nucleotide sequences to long reference sequences.
Exonerate exonerate is a generic tool for pairwise sequence comparison.
FastQC Quality control tool for high throughput sequence data.
GMAP (with GSNAP) - Genomic mapping and alignment GMAP (with GSNAP) - Genomic mapping and alignment package.
HMMER Homolog search and protein sequence alignments.
IMPUTE (genotype imputation) IMPUTE2 - Version 2 of IMPUTE for genotype imputation and haplotype phasing
InterProScan
JELLYFISH DNA substring (k-mer) counting.
Maker MAKER is a portable and easily configurable genome annotation pipeline.
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.
MrBayes Bayesian inference for phylogenetic and evolutionary models.
PLINK Analysis of genotype/phenotype data.
RAPSearch (protein similarity search) RAPSearch/RapSearch2 - Reduced Alphabet-based Protein similarity Search
RepeatMasker RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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.
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
Stacks Software pipeline for analysis of short-read genetic sequences for application to population genomics
TopHat Exon splice junction mapper based on BowTie RNA-Seq alignments.
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
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.
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.
Wannier90
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.
AutoDock A suite of programs for predicting how small molecules will bind to a target of known 3D structure.
CPMD Software for ab initio molecular dynamics. Users should be aware of the license requirements.
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.
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
LAMMPS LAMMPS, Large-scale Atomic/Molecular Massively Parallel Simulator
NAMD A molecular dynamics simulator for large biomolecular systems.
NWChem Scalable open-source solution for large scale molecular simulations.
ORCA An ab initio, DFT and semiempirical SCF-MO package.
Phonopy Phonopy is an open source package of phonon calculations based on the supercell approach.
Quantum ESPRESSO A suite of programs for electronic structure and materials modelling.
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.
XCrySDen XCrySDen is a crystalline and molecular structure visualisation program
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
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.
Octave A general purpose numerical package that is largely compatible with MATLAB.
OpenFOAM, OpenFOAM+ and OpenFOAM Extend Toolkit for building CFD applications.
Seismic Un*x An open source collection of software for seismic processing and research.
WRF Weather Research & Forecasting Model, including WPS (WRF Pre-processing system), WRF-Chem and WRF EMS (Environmental Modeling System).
Software Category: Programming
Software Brief Description
GNU binutils The GNU Binutils are a collection of binary tools.
Swig SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
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)
Expat Expat is an XML parser library written in C.
gdb GNU debugger.
Git Version control system.
idb Intel debugger.
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.
Mercurial Distributed version control system
Mono (C# environment) Mono .NET environment to provide a platform for running C# programs.
OpenCV
Perl Perl is a family of high-level, general-purpose, interpreted, dynamic programming languages.
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
Subversion An open source alternative to CVS for managing files for large development projects.
Xerces-C++ XML parser and writer.
Software Category: Mathematical Libraries and Applications
Software Brief Description
Lis Lis (Library of Iterative Solvers for linear systems, pronounced [lis]) is a parallel software library for solving linear equations and eigenvalue problems that arise in the numerical solution of partial differential equations using iterative methods.
BLAS Basic Linear Algebra Subprograms.
CGAL A C++ library for geometric algorithms.
FFTW A widely-used FFT implementation.
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.
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.
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.
MPFR The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
muParser muParser is an extensible high performance math expression parser library written in C++.
NetworkX A Python-based package for creating and analyzing graphs (networks of nodes and edges).
OpenBUGS Bayesian inference Using Gibbs Sampling using Markov Chain Monte Carlo (MCMC) simulation.
PETSc Toolkit for parallel solution of differential equations.
R Software environment and language for statistical data analysis.
ScaLAPACK ScaLAPACK is a parallelized subset of the LAPACK linear algebra package.
SCOTCH Graph and mesh partitioning, sparse matrix ordering.
Trilinos Object-oriented framework for linear algebra, meshing, preconditioners, solvers.
Software Category: Files and Data
Software Brief Description
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 5 Hierarchical Data Format - file format for storing a variety of data types.
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.
Vim An enhanced version of the vi text editor.
Software Category: Graphics
Software Brief Description
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.
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.
Qt Application and user interface development framework.
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.
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.
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.
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.
sh
tcsh It is a command language interpreter usable both as an interactive login shell and a shell script command processor.