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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 | |
|---|---|---|
| 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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). |