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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 | 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. |
| Software | Brief Description | |
|---|---|---|
| ABAQUS | Comprehensive finite element modelling package | |
| 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. | |
| 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 | Brief Description | |
|---|---|---|
| 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. | |
| ATSAS | A program suite for small-angle scattering data analysis from biological macromolecules | |
| AutoDock | A suite of programs for predicting how small molecules will bind to a target of known 3D structure. | |
| AutoDock_vina | AutoDock Vina is an open-source program for doing molecular docking. | |
| 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. | |
| GROMACS | A molecular dynamics program (along with attendant utilities) designed for simulations of large molecules, such as proteins. | |
| Gulp | GULP is a program for performing a variety of types of simulation on materials | |
| LAMMPS | LAMMPS, Large-scale Atomic/Molecular Massively Parallel Simulator | |
| Memprot | Memprot is a program that aims to fit Small Angle X-ray Scattering curves of detergent solubilized membrane proteins. | |
| NAMD | A molecular dynamics simulator for large biomolecular systems. | |
| NWChem | Scalable open-source solution for large scale molecular simulations. | |
| openkim | The KIM API is an Application Programming Interface for atomistic 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. | |
| 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. | |
| 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. | |
| ShengBTE - solving Boltzmann Transport Equation for phonons | ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons. | |
| 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. | |
| 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. | |
| VASP | An ab-initio quantum-mechanical molecular dynamics package based on pseudopotentials and a plane wave basis set. | |
| Wannier90 | ||
| XCrySDen | XCrySDen is a crystalline and molecular structure visualisation program |
| Software | Brief Description | |
|---|---|---|
| ABySS | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. See also Trans-ABySS below. | |
| 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). | |
| Augustus | AUGUSTUS is a gene prediction program for eukaryotes. | |
| 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. | |
| 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. | |
| bgc | bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci. | |
| 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. | |
| 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. | |
| Bowtie | Short read DNA sequence aligner. | |
| Bowtie2 | Short read DNA sequence aligner. | |
| BWA | Burrows-Wheeler Aligner - Aligns short nucleotide sequences to long reference sequences. | |
| 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. | |
| 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. | |
| 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. | |
| HMMER | Homolog search and protein sequence alignments. | |
| HTSlib | A C library for reading/writing high-throughput sequencing data | |
| IMPUTE (genotype imputation) | IMPUTE2 - Version 2 of IMPUTE for genotype imputation and haplotype phasing | |
| InterProScan | ||
| JELLYFISH | DNA substring (k-mer) counting. | |
| 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. | |
| Maker | MAKER is a portable and easily configurable genome annotation pipeline. | |
| 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 | |
| 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. | |
| 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. | |
| MrBayes | Bayesian inference for phylogenetic and evolutionary 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. | |
| PHAST (Phylogenic Analysis with Space/Time Models) | PHAST (Phylogenic Analysis with Space/Time Models) | |
| PLINK | Analysis of genotype/phenotype data. | |
| PRINSEQ | PReprocessing and INformation of SEQuence data | |
| RAPSearch (protein similarity search) | RAPSearch/RapSearch2 - Reduced Alphabet-based Protein similarity Search | |
| 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). | |
| RepeatMasker | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. | |
| RNAmmer | RNAmmer predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome 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 | |
| SignalP | SignalP 4.1 predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms | |
| 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 | |
| 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 | |
| TopHat | Exon splice junction mapper based on BowTie RNA-Seq alignments. | |
| 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. | |
| Treemix | TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. | |
| Trimmomatic | A flexible read trimming tool for Illumina NGS data | |
| 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 | Brief Description | |
|---|---|---|
| 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. | |
| 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. | |
| 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 | Brief Description | |
|---|---|---|
| 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. | |
| GNU binutils | The GNU Binutils are a collection of binary tools. | |
| 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. | |
| Swig | SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. | |
| Xerces-C++ | XML parser and writer. |
| Software | Brief Description | |
|---|---|---|
| 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. | |
| parallel-netcdf | A Parallel I/O Library for NetCDF File Access | |
| Szip | A library for lossless compression of scientific data. | |
| Vim | An enhanced version of the vi text editor. |
| 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. |