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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: Bioinformatics / Genomics Applications
Software Brief Description
DosageConverter DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther formats such as MaCH or PLINK.
ABySS Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. See also Trans-ABySS below.
ARB Sequence database handling and phylogenic analysis.
BEAST BEAST (Bayesian Evolutionary Analysis by Sampling Trees).
BioPerl Collection of Perl-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.
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.
Clustal Omega Clustal Omega - Multiple protein sequence alignment
Cufflinks Transcript assembly from RNA-Seq data.
FastQC Quality control tool for high throughput sequence data.
GATK "The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data."
HMMER Homolog search and protein sequence alignments.
IMPUTE (genotype imputation) IMPUTE2 - Version 2 of IMPUTE for genotype imputation and haplotype phasing
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.
Nemo Stochastic simulation to study evolution of life history/phenotypic traits and population genetics.
PLINK Analysis of genotype/phenotype data.
Ray De novo genome assembly.
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
SNPTEST SNPTEST - Program for whole-genome SNP association studies
TopHat Exon splice junction mapper based on BowTie RNA-Seq alignments.
Trans-ABySS A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.
Software Category: Chemistry and Biochemistry Applications
Software Brief Description
GROMACS A molecular dynamics program (along with attendant utilities) designed for simulations of large molecules, such as proteins.
CP2K Software for ab initio molecular dynamics based on mixed plane waves and Gaussian basis sets.
GAMESS A general molecular ab initio quantum chemistry package
LAMMPS LAMMPS, Large-scale Atomic/Molecular Massively Parallel Simulator
Molden A visualization, pre- and post-processing program for molecular and electronic structure.
NAMD A molecular dynamics simulator for large biomolecular systems.
NWChem Scalable open-source solution for large scale molecular simulations.
Quantum ESPRESSO A suite of programs for electronic structure and materials modelling.
SIESTA An electronic structure (periodic, linear scaling DFT) code and molecular dynamics package.
Yambo Ab initio code for quasi-particle excited state energies and optical properties for solid state and molecular physics applications.
Software Category: Programming
Software Brief Description
Boost An eclectic collection of C++ libraries.
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)
gdb GNU debugger.
GNU libgomp GNU implementation of the OpenMP Application Programming Interface (API).
idb Intel debugger.
Java Java is a programming language and computing platform.
Mercurial Distributed version control system
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.
Ruby A dynamic, interpreted, open source programming language with a focus on simplicity and productivity.
Subversion An open source alternative to CVS for managing files for large development projects.
Software Category: Files and Data
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.
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.
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.
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.
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.
NCAR Graphics and NCL Libraries and utilities for contour maps, vector and streamline plots, X-Y graphs, map databases, etc.
Netpbm Image conversion utilities and library.
VTK - Visualization Toolkit Comprehensive libraries for visualization of many types of multi-dimensional data.
zlib Data compression library.
Software Category: Mathematical Libraries and Applications
Software Brief Description
BLAS Basic Linear Algebra Subprograms.
FFTW A widely-used FFT implementation.
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.
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.
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.
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.
SLEPc PETSc add-on eigenvalue solver for large sparse systems.
SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers) SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers)
Software Category: UNIX Environment
Software Brief Description
64-bit Scientific Linux An operating system distributed by CERN that is similar to and compatible with CentOS.
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.
zsh Zsh is a shell designed for interactive use, although it is also a powerful scripting language.
Software Category: Other Applications
Software Brief Description
Gadget Simulation of cosmological structure formation.
GDAL Geospatial Data Abstraction Library.
libLAS ASPRS LiDAR data translation tools.
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.
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
WRF Weather Research & Forecasting Model, including WPS (WRF Pre-processing system), WRF-Chem and WRF EMS (Environmental Modeling System).