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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 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 | Brief Description | |
|---|---|---|
| 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. | |
| dl_meso | The DL_MESO Mesoscale Simulation Package | |
| 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 | |
| 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 | |
| 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. | |
| 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. | |
| 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 | Brief Description | |
|---|---|---|
| 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. | |
| 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 | |
| GMAP (with GSNAP) - Genomic mapping and alignment | GMAP (with GSNAP) - Genomic mapping and alignment package. | |
| hisat2 | graph-based alignment of next generation sequencing reads to a population of genomes | |
| HMMER | Homolog search and protein sequence alignments. | |
| IMa2 | Isolation and migration effects in population genetics. | |
| Ima2p | ||
| Image | Iterative Mapping and Assembly for Gap Elimination | |
| LepMAP | ||
| 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. | |
| orthomcl | ||
| 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. | |
| 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. | |
| 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. | |
| 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 | |
| TMHMM | Prediction of transmembrane helices in proteins | |
| 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 | 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 | 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). |
| 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 | 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. | |
| 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 | 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 | |
| Hadoop | Tool for map/reduce-style calculations | |
| 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 | Brief Description | |
|---|---|---|
| MySQL | MySQL is a popular open source database | |
| PostgreSQL | PostgreSQL is a powerful, open source object-relational database system. |