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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: Chemistry and Biochemistry Applications
Software Brief Description
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.
ShengBTE - solving Boltzmann Transport Equation for phonons ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons.
ABINIT Electronic structure calculations, based on Density Functional Theory, for the treatment of molecules and periodic solids.
Amber A suite of programs for molecular calculations, including molecular dynamics.
ASE ASE is an Atomistic Simulation Environment written in the Python
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.
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.
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
Gulp GULP is a program for performing a variety of types of simulation on materials
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.
Open Babel Data conversion toolkit.
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.
VASP An ab-initio quantum-mechanical molecular dynamics package based on pseudopotentials and a plane wave basis set.
YAeHMOP Yet Another extended Huckel Molecular Orbital Package.
Software Category: Bioinformatics / Genomics Applications
Software Brief Description
FastTree FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
freebayes
GapCloser The GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenevo
hisat2 graph-based alignment of next generation sequencing reads to a population of genomes
Ima2p
Image Iterative Mapping and Assembly for Gap Elimination
LepMAP
orthomcl
RNAmmer RNAmmer predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.
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.
TMHMM Prediction of transmembrane helices in proteins
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.
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.
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.
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.
Cufflinks Transcript assembly from RNA-Seq data.
ExaML/RAxML - Phylogenetic tree analysis Phylogenetic tree analysis.
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.
MEME Suite Identify motifs (patterns) in sequences.
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.
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
QIIME Quantitative Insights into Microbial Ecology.
RITA Rapid Identification of Taxonomic Assignments. Nucleotide sequence analysis.
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.
SOAPdenovo Short Oligonucleotide Analysis Package for Illumina GA short-read assembly.
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.
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.
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.
Software Category: Files and Data
Software Brief Description
Hadoop Tool for map/reduce-style calculations
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.
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: 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: Programming
Software Brief Description
Blitz++ C++ template library for dense vectors and multi-dimensional arrays.
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)
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 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
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.
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: Graphics
Software Brief Description
Circos Oriented towards genomic data display but can be applied to other data.
Gbrowse GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.
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
Matplotlib Python-based 2D (mostly) plotting library.
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.
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.
Qt Application and user interface development framework.
Rasmol Molecular graphics visualization.
VISAT An image processing and data analysis program for remotely sensed data.
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: 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.
FFTW A widely-used FFT implementation.
FreeFem++ - Partial Differential Equation Solver FreeFem++ is typically applied to solve multiphysics non-linear systems.
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.
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.
MUMPS Parallel direct solver for sparse systems.
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.
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.
SCOTCH Graph and mesh partitioning, sparse matrix ordering.
SLEPc PETSc add-on eigenvalue solver for large sparse systems.
SuiteSparse a Suite of sparse matrix packages
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 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.
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.
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
BEAM A toolbox for viewing and analyzing remotely-sensed data.
GDAL Geospatial Data Abstraction Library.
GRIB-API GRIB-API is an API for working with GRIB meteorological data format.
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.
MOM The Modular Ocean Model (MOM) is a numerical ocean model based on the hydrostatic primitive equations.
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.
WRF Weather Research & Forecasting Model, including WPS (WRF Pre-processing system), WRF-Chem and WRF EMS (Environmental Modeling System).