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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
WebLogo WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.
Velvet Package for genomic sequence assembly from short-read data.
VCFtools a program package designed for working with VCF files
VarSim A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications.
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.
Trinity De novo reconstruction of transcriptomes from RNA-seq data.
Trimmomatic A flexible read trimming tool for Illumina NGS data
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.
Trans-ABySS A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.
TopHat Exon splice junction mapper based on BowTie RNA-Seq alignments.
TMHMM Prediction of transmembrane helices in proteins
Tandem Repeats Finder Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
Structure The program structure is a free software package for using multi-locus genotype data to investigate population structure.
Stacks Software pipeline for analysis of short-read genetic sequences for application to population genomics
SPAdes Genome Assembler SPAdes - assembler for bacterial genomes
SOAPdenovo-Trans SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.
SNAP (Semi-HMM-based Nucleic Acid Parser) gene prediction tool.
SignalP SignalP 4.1 predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms
SAMtools and HTSlib utilities SAMtools is a set of utilities for manipulating SAM (Sequence Alignment/Map) format files.
RSEM Package for estimating gene and isoform expression levels from RNA-Seq data.
RNAmmer RNAmmer predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.
RMBlast RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite.
RepeatMasker RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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).
Ray De novo genome assembly.
Picard tools Java-based tools for manipulation of BAM (Binary sequence alignment map) data files.
Mothur Bioinformatics software for microbial ecology.
Minia Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.
MEGAHIT An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
Kraken Kraken is a Taxonomic Sequence Classification System
JELLYFISH DNA substring (k-mer) counting.
IQ-TREE (phylogenetics) IQ-TREE is a phylogenetics package for inferring maximum likelihood trees.
Homer HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis.
HMMER Homolog search and protein sequence alignments.
hisat2 graph-based alignment of next generation sequencing reads to a population of genomes
GMAP (with GSNAP) - Genomic mapping and alignment GMAP (with GSNAP) - Genomic mapping and alignment package.
GATK "The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data."
freebayes
FastQC Quality control tool for high throughput sequence data.
Exonerate exonerate is a generic tool for pairwise sequence comparison.
ESTScan ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality.
Cufflinks Transcript assembly from RNA-Seq data.
Celera Whole-Genome Shotgun Assembler Celera whole-genome shotgun sequence assembler and conversion utilities.
Cd-hit CD-HIT is a program for clustering DNA/protein sequence database at high identity with tolerance.
CAP3 A DNA Sequence Assembly Program
BWA Burrows-Wheeler Aligner - Aligns short nucleotide sequences to long reference sequences.
Bowtie2 Short read DNA sequence aligner.
Bowtie Short read DNA sequence aligner.
BLAT BLAST-Like Alignment Tool. See the BLAT site for more information.
BLAST A suite of tools for assessing the similarity of a given sequence of proteins or nucleotides with a database of sequences.
BEDTools Utility suite for comparing genomic features.
BCFtools (VCF/BCF file manipulation) BCFtools is a set of utilities for manipulating Variant Call Format and related files.
bamUtil bamUtil is a repository that contains several programs that perform operations on SAM/BAM files.
Augustus AUGUSTUS is a gene prediction program for eukaryotes.
ALLPATHS-LG Sequence assembly program.
ABySS Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. See also Trans-ABySS below.
Software Category: Graphics
Software
Brief Description
VTK - Visualization Toolkit Comprehensive libraries for visualization of many types of multi-dimensional data.
VMD VMD is a program for displaying and animating large biomolecular systems.
ImageMagick Software suite for image format conversion and editing.
Gnuplot Command-driven x-y plotting program, generally of lower quality than xmgrace, but offering some 3D features.
Eye of GNOME Image viewer (eog).
Software Category: Files and Data
Software
Brief Description
Vim An enhanced version of the vi text editor.
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.
nano A simple non-graphical text editor with on-screen reminders for commonly-used commands (similar to pico).
HDF 5 Hierarchical Data Format - file format for storing a variety of data types.
gedit - graphical text editor gedit - graphical text editor with syntax highlighting
Emacs GNU version of this common text editor.
Software Category: UNIX Environment
Software
Brief Description
tcsh It is a command language interpreter usable both as an interactive login shell and a shell script command processor.
sh
Parallel GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
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.
csh The improved version of tcsh.
64-bit SLES 11 A Linux-based operating system designed for servers, mainframes, and workstations.
Software Category: Programming
Software
Brief Description
Swig SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
Subversion An open source alternative to CVS for managing files for large development projects.
Ruby A dynamic, interpreted, open source programming language with a focus on simplicity and productivity.
Python Python is an interactive, object-oriented, extensible programming language.
Perl Perl is a family of high-level, general-purpose, interpreted, dynamic programming languages.
LibYAML LibYAML is a YAML 1.1 parser and emitter written in C.
Julia Julia is a high-level, dynamic language for technical computing
Java Java is a programming language and computing platform.
Jam Make replacement for C/C++ projects.
idb Intel debugger.
Git Version control system.
gdb GNU debugger.
Compilers - C, C++ and Fortran Compilers - C (gcc, icc, pgcc), C++ (g++, icpc, pgCC), Fortran (gfortran, ifort, pgf77, pgf90, pgf95)
CMake Cross platform software build system
Boost An eclectic collection of C++ libraries.
Software Category: Mathematical Libraries and Applications
Software
Brief Description
ScaLAPACK ScaLAPACK is a parallelized subset of the LAPACK linear algebra package.
R Software environment and language for statistical data analysis.
PETSc Toolkit for parallel solution of differential equations.
NetworkX A Python-based package for creating and analyzing graphs (networks of nodes and edges).
Nektar++ Framework for partial differential equation solvers based on finite-element methods.
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.
Mathematica A comprehensive system for mathematical calculations.
LAPACK Linear algebra subroutine package.
JAGS Just Another Gibbs Sampler - analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.
GSL A numerical library for C and C++ programmers including numerical integration, linear algebra, minimization, special functions and other mathematical routines.
FFTW A widely-used FFT implementation.
FEniCS A framework for solution of differential equations by finite element methods. DOLFIN is a key component of the FEniCS environment.
BLAS Basic Linear Algebra Subprograms.
Software Category: Chemistry and Biochemistry Applications
Software
Brief Description
NWChem Scalable open-source solution for large scale molecular simulations.
GROMACS A molecular dynamics program (along with attendant utilities) designed for simulations of large molecules, such as proteins.
Gaussian A suite of programs for semi-empirical and ab initio molecular orbital calculations.
CPMD Software for ab initio molecular dynamics. Users should be aware of the license requirements.
CP2K Software for ab initio molecular dynamics based on mixed plane waves and Gaussian basis sets.
Chaste Cancer, Heart and Soft Tissue Environment - tissue and cell level electro-physiology, discrete and soft tissue modelling.
Software Category: Other Applications
Software
Brief Description
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.