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Software Overview

National Systems


WestGrid Systems





All WestGrid Software

Software Category: Bioinformatics / Genomics Applications
Software Brief Description
ARB Sequence database handling and phylogenic analysis.
BEAST BEAST (Bayesian Evolutionary Analysis by Sampling Trees).
BioPerl Collection of Perl-based tools for bioinformatics.
Bowtie Short read DNA sequence aligner.
Bowtie2 Short read DNA sequence aligner.
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.
HMMER Homolog search and protein sequence alignments.
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.
SNPTEST SNPTEST - Program for whole-genome SNP association studies
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
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
ROOT (data analysis framework) ROOT is an object-oriented framework aimed at solving the data analysis challenges of high-energy physics.
Software Category: Files and Data
Software Brief Description
Emacs GNU version of this common text editor.
jEdit A graphical editor for programmers (requires X Windows).
NCO A set of programs for manipulating data in NetCDF files.
NEdit A graphical editor recommended for PC users, but requires X Windows.
Szip A library for lossless compression of scientific data.
Vim An enhanced version of the vi text editor.
Software Category: Graphics
Software Brief Description
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).
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.
LAPACK Linear algebra subroutine package.
PETSc Toolkit for parallel solution of differential equations.
R Software environment and language for statistical data analysis.
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.
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.
Software Category: Other Applications
Software Brief Description
Gadget Simulation of cosmological structure formation.
GDAL Geospatial Data Abstraction Library.
libLAS ASPRS LiDAR data translation tools.
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).