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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.

New software requests on WestGrid systems are no longer being accepted.  You are responsible for installing new software in your own directory.

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: Programming
Software
Brief Description
Xerces-C++ XML parser and writer.
Swig SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
Subversion An open source alternative to CVS for managing files for large development projects.
SCons SCons is an Open Source software construction tool
Ruby A dynamic, interpreted, open source programming language with a focus on simplicity and productivity.
RStudio Integrated Development Environment for R
ROOT (data analysis framework) ROOT is an object-oriented framework aimed at solving the data analysis challenges of high-energy physics.
Python Python is an interactive, object-oriented, extensible programming language.
Perl Perl is a family of high-level, general-purpose, interpreted, dynamic programming languages.
OpenCV
Mono (C# environment) Mono .NET environment to provide a platform for running C# programs.
Mercurial Distributed version control system
LibYAML LibYAML is a YAML 1.1 parser and emitter written in C.
Julia Julia is a high-level, dynamic language for technical computing
Java Java is a programming language and computing platform.
idb Intel debugger.
GNU binutils The GNU Binutils are a collection of binary tools.
Git Version control system.
gdb GNU debugger.
Expat Expat is an XML parser library written in C.
Compilers - C, C++ and Fortran Compilers - C (gcc, icc, pgcc), C++ (g++, icpc, pgCC), Fortran (gfortran, ifort, pgf77, pgf90, pgf95)
CMake Cross platform software build system
CLAPACK F2C translation of LAPACK
Boost An eclectic collection of C++ libraries.
Software Category: Chemistry and Biochemistry Applications
Software
Brief Description
XCrySDen XCrySDen is a crystalline and molecular structure visualisation program
Wannier90
VASP An ab-initio quantum-mechanical molecular dynamics package based on pseudopotentials and a plane wave basis set.
Spglib Spglib is a C library for finding and handling crystal symmetries.
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.
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.
SIESTA An electronic structure (periodic, linear scaling DFT) code and molecular dynamics package.
ShengBTE - solving Boltzmann Transport Equation for phonons ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons.
Rosetta Software Suite Protein design and analysis. Write to WestGrid support for access information.
Quantum ESPRESSO A suite of programs for electronic structure and materials modelling.
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.
Phonopy Phonopy is an open source package of phonon calculations based on the supercell approach.
ORCA An ab initio, DFT and semiempirical SCF-MO package.
openkim The KIM API is an Application Programming Interface for atomistic simulations.
NWChem Scalable open-source solution for large scale molecular simulations.
NAMD A molecular dynamics simulator for large biomolecular systems.
Memprot Memprot is a program that aims to fit Small Angle X-ray Scattering curves of detergent solubilized membrane proteins.
LAMMPS LAMMPS, Large-scale Atomic/Molecular Massively Parallel Simulator
Gulp GULP is a program for performing a variety of types of simulation on materials
GROMACS A molecular dynamics program (along with attendant utilities) designed for simulations of large molecules, such as proteins.
Gaussian A suite of programs for semi-empirical and ab initio molecular orbital calculations.
Gar2ped a Gaussian 94 output postprocessing utility
GAMESS A general molecular ab initio quantum chemistry package
Elk An electronic structure code for determining the properties of crystalline solids.
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".
CPMD Software for ab initio molecular dynamics. Users should be aware of the license requirements.
AutoDock_vina AutoDock Vina is an open-source program for doing molecular docking.
AutoDock A suite of programs for predicting how small molecules will bind to a target of known 3D structure.
ATSAS A program suite for small-angle scattering data analysis from biological macromolecules
Amber A suite of programs for molecular calculations, including molecular dynamics.
Adaptive Poisson-Boltzmann Solver (APBS) Software for modelling biomolecular solvation.
ABINIT Electronic structure calculations, based on Density Functional Theory, for the treatment of molecules and periodic solids.
Software Category: Other Applications
Software
Brief Description
WRF Weather Research & Forecasting Model, including WPS (WRF Pre-processing system), WRF-Chem and WRF EMS (Environmental Modeling System).
Seismic Un*x An open source collection of software for seismic processing and research.
OpenFOAM, OpenFOAM+ and OpenFOAM Extend Toolkit for building CFD applications.
Octave A general purpose numerical package that is largely compatible with MATLAB.
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.
Geant4 Geant4 is a toolkit for the simulation of the passage of particles through matter.
GATE GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to numerical simulations in medical imaging and radiotherapy.
CompuCell3D CompuCell3D is an open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms.
CLHEP A Class Library for High Energy Physics
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.
ABAQUS Comprehensive finite element modelling package
Software Category: Bioinformatics / Genomics Applications
Software
Brief Description
WHAM/WHAMG - WHole-genome Alignment Metrics WHAM/WHAMG - WHole-genome Alignment Metrics for structural variant detection and association testing
VCFtools a program package designed for working with VCF files
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.
Trinity De novo reconstruction of transcriptomes from RNA-seq data.
Trimmomatic A flexible read trimming tool for Illumina NGS data
Treemix TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.
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.
TopHat Exon splice junction mapper based on BowTie RNA-Seq alignments.
TMHMM Prediction of transmembrane helices in proteins
SVDetect A tool to identify genomic structural variations from paired-end and mate-pair sequencing data
Subread Subread package: high-performance read alignment, quantification and mutation discovery
Structure The program structure is a free software package for using multi-locus genotype data to investigate population structure.
Stacks Software pipeline for analysis of short-read genetic sequences for application to population genomics
SNPTEST SNPTEST - Program for whole-genome SNP association studies
SNAP (Semi-HMM-based Nucleic Acid Parser) gene prediction tool.
SignalP SignalP 4.1 predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms
SHAPEIT (estimation of haplotypes) SHAPEIT - Halotype estimation (phasing) from genotype or sequencing data
SAMtools and HTSlib utilities SAMtools is a set of utilities for manipulating SAM (Sequence Alignment/Map) format files.
RSEM Package for estimating gene and isoform expression levels from RNA-Seq data.
RNAmmer RNAmmer predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.
RepeatMasker RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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).
RAPSearch (protein similarity search) RAPSearch/RapSearch2 - Reduced Alphabet-based Protein similarity Search
PRINSEQ PReprocessing and INformation of SEQuence data
PLINK Analysis of genotype/phenotype data.
PHAST (Phylogenic Analysis with Space/Time Models) PHAST (Phylogenic Analysis with Space/Time Models)
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.
MrBayes Bayesian inference for phylogenetic and evolutionary models.
Minimac3 Minimac3 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and minimac2.
Minimac2 minimac2 is an improved version of Minimac.
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.
Megan Stand-alone analysis tool for metagenomic of short-read data
MEGAHIT An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
Maker MAKER is a portable and easily configurable genome annotation pipeline.
Mach MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.
Kraken Kraken is a Taxonomic Sequence Classification System
JELLYFISH DNA substring (k-mer) counting.
InterProScan
IMPUTE (genotype imputation) IMPUTE2 - Version 2 of IMPUTE for genotype imputation and haplotype phasing
HTSlib A C library for reading/writing high-throughput sequencing data
HMMER Homolog search and protein sequence alignments.
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.
GMAP (with GSNAP) - Genomic mapping and alignment GMAP (with GSNAP) - Genomic mapping and alignment package.
FastQC Quality control tool for high throughput sequence data.
Exonerate exonerate is a generic tool for pairwise sequence comparison.
DosageConverter DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther formats such as MaCH or PLINK.
DiScRIBinATE
CNVnator a tool for CNV discovery and genotyping from depth of read mapping.
BWA Burrows-Wheeler Aligner - Aligns short nucleotide sequences to long reference sequences.
Bowtie2 Short read DNA sequence aligner.
Bowtie Short read DNA sequence aligner.
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.
BLAT BLAST-Like Alignment Tool. See the BLAT site for more information.
BLAST A suite of tools for assessing the similarity of a given sequence of proteins or nucleotides with a database of sequences.
bgc bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci.
BEAGLE (beagle-lib) Broad-platform Evolutionary Analysis General Likelihood Evaluator - library for speeding up phylogenetic calculations.
BCFtools (VCF/BCF file manipulation) BCFtools is a set of utilities for manipulating Variant Call Format and related files.
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.
Augustus AUGUSTUS is a gene prediction program for eukaryotes.
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).
ADMIXTURE ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.
ABySS Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. See also Trans-ABySS below.
Software Category: Graphics
Software
Brief Description
VTK - Visualization Toolkit Comprehensive libraries for visualization of many types of multi-dimensional data.
VMD VMD is a program for displaying and animating large biomolecular systems.
Qt Application and user interface development framework.
Ncview Visual browser for NetCDF files.
NCAR Graphics and NCL Libraries and utilities for contour maps, vector and streamline plots, X-Y graphs, map databases, etc.
ImageMagick Software suite for image format conversion and editing.
Grace/Xmgrace GUI-based x-y plotting for thesis and publication-quality graphs.
Gnuplot Command-driven x-y plotting program, generally of lower quality than xmgrace, but offering some 3D features.
Software Category: Files and Data
Software
Brief Description
Vim An enhanced version of the vi text editor.
Szip A library for lossless compression of scientific data.
parallel-netcdf A Parallel I/O Library for NetCDF File Access
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.
NEdit A graphical editor recommended for PC users, but requires X Windows.
NCO A set of programs for manipulating data in NetCDF files.
nano A simple non-graphical text editor with on-screen reminders for commonly-used commands (similar to pico).
HDF 5 Hierarchical Data Format - file format for storing a variety of data types.
gedit - graphical text editor gedit - graphical text editor with syntax highlighting
Emacs GNU version of this common text editor.
Climate Data Operators (CDO) A command line suite for manipulating and analysing climate data.
Software Category: Mathematical Libraries and Applications
Software
Brief Description
Trilinos Object-oriented framework for linear algebra, meshing, preconditioners, solvers.
SCOTCH Graph and mesh partitioning, sparse matrix ordering.
ScaLAPACK ScaLAPACK is a parallelized subset of the LAPACK linear algebra package.
R Software environment and language for statistical data analysis.
PETSc Toolkit for parallel solution of differential equations.
OpenBUGS Bayesian inference Using Gibbs Sampling using Markov Chain Monte Carlo (MCMC) simulation.
NetworkX A Python-based package for creating and analyzing graphs (networks of nodes and edges).
muParser muParser is an extensible high performance math expression parser library written in C++.
MPFR The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
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.
Mathematica A comprehensive system for mathematical calculations.
Maple Mathematical computation engine
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.
LAPACK Linear algebra subroutine package.
JAGS Just Another Gibbs Sampler - analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.
GSL A numerical library for C and C++ programmers including numerical integration, linear algebra, minimization, special functions and other mathematical routines.
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.
FFTW A widely-used FFT implementation.
CGAL A C++ library for geometric algorithms.
BLAS Basic Linear Algebra Subprograms.
Software Category: UNIX Environment
Software
Brief Description
tcsh It is a command language interpreter usable both as an interactive login shell and a shell script command processor.
sh
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.
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.
Intel MPI A multi-fabric message passing library that implements the Message Passing Interface.
csh The improved version of tcsh.
bash (default) Bash is a Unix shell.
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.