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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 | Brief Description | |
|---|---|---|
| ADMIXTURE | ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. | |
| Annovar | ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). | |
| BamTools | BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files. | |
| bamUtil | bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. | |
| bgc | bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci. | |
| BMTagger | Best Match Tagger (BMTagger) is an efficient tool that discriminates between human reads and microbial reads without doing an alignment of all reads to the human genome. | |
| Bridger | ||
| CAP3 | A DNA Sequence Assembly Program | |
| CNVnator | a tool for CNV discovery and genotyping from depth of read mapping. | |
| DiScRIBinATE | ||
| DosageConverter | DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther formats such as MaCH or PLINK. | |
| ESTScan | ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. | |
| FastTree | FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. | |
| freebayes | ||
| FStitch | This software is written primarily for scientists looking to identify putative nascent transcripts de novo in Global Run-On sequencing. | |
| GapCloser | The GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenevo | |
| GOTTCHA | GOTTCHA (Genomic Origin Through Taxonomic CHAllenge) is an application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly smaller false discovery rates (FDR) that is also laptop deployable. | |
| hisat2 | graph-based alignment of next generation sequencing reads to a population of genomes | |
| Homer | HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. | |
| HTSlib | A C library for reading/writing high-throughput sequencing data | |
| IDBA-UD | IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data | |
| Ima2p | ||
| Image | Iterative Mapping and Assembly for Gap Elimination | |
| Kraken | Kraken is a Taxonomic Sequence Classification System | |
| LepMAP | ||
| Mach | MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. | |
| MEGAHIT | An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph | |
| Megan | Stand-alone analysis tool for metagenomic of short-read data | |
| MetaVelvet | MetaVelvet identifies shared nodes (named chimeric nodes) between two subgraphs and disconnects two subgraphs by splitting the shared nodes. | |
| 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. | |
| Minimac2 | minimac2 is an improved version of Minimac. | |
| Minimac3 | Minimac3 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac and minimac2. | |
| orthomcl | ||
| PEAR | PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. | |
| PHAST (Phylogenic Analysis with Space/Time Models) | PHAST (Phylogenic Analysis with Space/Time Models) | |
| PRINSEQ | PReprocessing and INformation of SEQuence data | |
| 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). | |
| RNAmmer | RNAmmer predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences. | |
| SCUBAT | SCUBAT (Scaffolding Contigs Using BLAT And Transcripts) uses any set of transcripts to identify cases where a transcript is split over multiple genome fragments and attempts to use this information to scaffold the genome. | |
| 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. | |
| Structure | The program structure is a free software package for using multi-locus genotype data to investigate population structure. | |
| Subread | Subread package: high-performance read alignment, quantification and mutation discovery | |
| SVDetect | A tool to identify genomic structural variations from paired-end and mate-pair sequencing data | |
| TMHMM | Prediction of transmembrane helices in proteins | |
| 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. | |
| Trimmomatic | A flexible read trimming tool for Illumina NGS data | |
| VarSim | A high-fidelity simulation validation framework for high-throughput genome sequencing with cancer applications. | |
| WebLogo | WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible. | |
| 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. | |
| Augustus | AUGUSTUS is a gene prediction program for eukaryotes. | |
| BCFtools (VCF/BCF file manipulation) | BCFtools is a set of utilities for manipulating Variant Call Format and related files. | |
| bcl2fastq - Illumina BCL to FASTQ conversion utility | bcl2fastq - Illumina BCL to FASTQ conversion utility | |
| 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. | |
| biobambam | biobambam - a set of tools for processing BAM format sequence files. | |
| 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. | |
| BUCKy (phylogenetic analysis) | BUCKy - Bayesian phylogenetic analysis of gene tree concordance. | |
| 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. | |
| Clustal Omega | Clustal Omega - Multiple protein sequence alignment | |
| Coral | Error correction software for DNA sequence analysis. | |
| Cufflinks | Transcript assembly from RNA-Seq data. | |
| DIAMOND - sequence aligner | Program for local aligments of translated nucleotide or amino acid sequences to protein references | |
| DISCOVAR and DISCOVAR de novo - genome assembly | DISCOVAR de novo whole genome shotgun assembler from 250-base Illumina PCR-free fragment reads. | |
| ExaML/RAxML - Phylogenetic tree analysis | Phylogenetic tree analysis. | |
| Exonerate | exonerate is a generic tool for pairwise sequence comparison. | |
| FastQC | Quality control tool for high throughput sequence data. | |
| fastStructure (population genetics) | Infer population structure from large SNP genotype data. | |
| FASTX-Toolkit (sequence pre-processing) | FASTX-Toolkit - command line tools for short read sequence data pre-processing. | |
| GATK | "The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data." | |
| 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. | |
| IMPUTE (genotype imputation) | IMPUTE2 - Version 2 of IMPUTE for genotype imputation and haplotype phasing | |
| InterProScan | ||
| IQ-TREE (phylogenetics) | IQ-TREE is a phylogenetics package for inferring maximum likelihood trees. | |
| JELLYFISH | DNA substring (k-mer) counting. | |
| kSNP3 - find SNPs in DNA sequences and estimate phylogenetic trees | kSNP3 - Software to find single nucleotide polymorphisms in DNA sequences and estimate phylogenetic trees | |
| Maker | MAKER is a portable and easily configurable genome annotation pipeline. | |
| MaSuRCA - whole genome assembler | MaSuRCA whole genome assembler | |
| MEME Suite | Identify motifs (patterns) in sequences. | |
| MetAMOS | MetAMOS - framework for genome assembly and analysis. | |
| 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. | |
| MUMmer | Alignment of large DNA and protein sequences. | |
| 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 | |
| Picard tools | Java-based tools for manipulation of BAM (Binary sequence alignment map) data files. | |
| PLINK | Analysis of genotype/phenotype data. | |
| Prodigal | Prodigal: Prokaryotic Dynamic Programming Genefinding Algorithm | |
| QIIME | Quantitative Insights into Microbial Ecology. | |
| RAPSearch (protein similarity search) | RAPSearch/RapSearch2 - Reduced Alphabet-based Protein similarity Search | |
| Ray | De novo genome assembly. | |
| RepeatMasker | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. | |
| RITA | Rapid Identification of Taxonomic Assignments. Nucleotide sequence analysis. | |
| RMBlast | RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. | |
| 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. | |
| SGA | Memory efficient de novo assembler of high-coverage short-read sequence data for large genomes | |
| SHAPEIT (estimation of haplotypes) | SHAPEIT - Halotype estimation (phasing) from genotype or sequencing data | |
| SNAP | (Semi-HMM-based Nucleic Acid Parser) gene prediction tool. | |
| SNPTEST | SNPTEST - Program for whole-genome SNP association studies | |
| SOAPdenovo | Short Oligonucleotide Analysis Package for Illumina GA short-read assembly. | |
| 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. | |
| SPAdes Genome Assembler | SPAdes - assembler for bacterial genomes | |
| Stacks | Software pipeline for analysis of short-read genetic sequences for application to population genomics | |
| STAR | STAR: Spliced Transcripts Alignment to a Reference | |
| Tablet - Next Generation Sequence Assembly Visualization | Tablet is a graphical viewer for next generation sequence assemblies and alignments. | |
| Tandem Repeats Finder | Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. | |
| 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. | |
| Treemix | TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. | |
| 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. | |
| WHAM/WHAMG - WHole-genome Alignment Metrics | WHAM/WHAMG - WHole-genome Alignment Metrics for structural variant detection and association testing |
| Software | Brief Description | |
|---|---|---|
| ATSAS | A program suite for small-angle scattering data analysis from biological macromolecules | |
| AutoDock_vina | AutoDock Vina is an open-source program for doing molecular docking. | |
| 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. | |
| Memprot | Memprot is a program that aims to fit Small Angle X-ray Scattering curves of detergent solubilized membrane proteins. | |
| openkim | The KIM API is an Application Programming Interface for atomistic simulations. | |
| PLUMED | PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. | |
| ShengBTE - solving Boltzmann Transport Equation for phonons | ShengBTE is a software package for solving the Boltzmann Transport Equation for phonons. | |
| Smoldyn | Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. | |
| Spglib | Spglib is a C library for finding and handling crystal symmetries. | |
| Wannier90 | ||
| ABINIT | Electronic structure calculations, based on Density Functional Theory, for the treatment of molecules and periodic solids. | |
| Adaptive Poisson-Boltzmann Solver (APBS) | Software for modelling biomolecular solvation. | |
| Amber | A suite of programs for molecular calculations, including molecular dynamics. | |
| ASE | ASE is an Atomistic Simulation Environment written in the Python | |
| AutoDock | A suite of programs for predicting how small molecules will bind to a target of known 3D structure. | |
| BigDFT | A massively-parallel wavelet-based DFT code for solid state/nanoclusters modeling for material science. | |
| 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. | |
| Dalton | Together, the two programs, Dalton and LSDalton, provide an extensive functionality for the calculations of molecular properties at the HF, DFT, MCSCF, and CC levels of theory. Many of these properties are only available in the Dalton2016 suite. | |
| 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_POLY | DL_POLY is a suite of programs developed at Daresbury Laboratory for molecular dynamics simulations of a variety of systems, including "macromolecules, polymers, ionic systems and solutions". | |
| Elk | An electronic structure code for determining the properties of crystalline solids. | |
| 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 | |
| Gar2ped | a Gaussian 94 output postprocessing utility | |
| Gaussian | A suite of programs for semi-empirical and ab initio molecular orbital calculations. | |
| GPAW | ||
| Gulp | GULP is a program for performing a variety of types of simulation on materials | |
| HOOMD-blue particle simulation toolbox | HOOMD-blue - General purpose particle simulation toolkit. | |
| LAMMPS | LAMMPS, Large-scale Atomic/Molecular Massively Parallel Simulator | |
| MGLTools including AutoDockTools | MGLTools, including AutoDockTools (ADT) is a suite of programs for molecular structure visualization and analysis. | |
| Molden | A visualization, pre- and post-processing program for molecular and electronic structure. | |
| MOPAC | MOPAC (Molecular Orbital PACkage) is a general-purpose semiempirical quantum chemistry package for the study of solid state and molecular structures and reactions. | |
| NAMD | A molecular dynamics simulator for large biomolecular systems. | |
| NBO | NBO: Natural Bond Orbital analysys program | |
| NEURON | An environment for simulating neurons and networks of neurons. | |
| NWChem | Scalable open-source solution for large scale molecular simulations. | |
| Open Babel | Data conversion toolkit. | |
| OpenMX | Open Materials Explorer - O(N) massively parallel DFT code for nano-scale material science. | |
| ORCA | An ab initio, DFT and semiempirical SCF-MO package. | |
| PDB2PQR | Preparing structures for continuum electrostatics calculations. | |
| Phonopy | Phonopy is an open source package of phonon calculations based on the supercell approach. | |
| Priroda | Priroda is a fast parallel relativistic DFT/ab initio code for molecular modeling | |
| PSI | PSI is an open-source suite of ab initio quantum chemistry programs | |
| Qbox DFT | Based electronic structure and molecular dynamics program. | |
| Quantum ESPRESSO | A suite of programs for electronic structure and materials modelling. | |
| QWalk | QWalk is an efficient Quantum Monte Carlo code by the group of Lucas Wagner | |
| 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. | |
| Sire | Sire is a free, open source, multiscale molecular simulation framework, written to allow computational modelers to quickly prototype and develop new algorithms for molecular simulation and molecular design. | |
| VASP | An ab-initio quantum-mechanical molecular dynamics package based on pseudopotentials and a plane wave basis set. | |
| WebMO | WebMO is a web portal for running and visualization of Computational Chemistry computations | |
| XCrySDen | XCrySDen is a crystalline and molecular structure visualisation program | |
| YAeHMOP | Yet Another extended Huckel Molecular Orbital Package. | |
| Yambo | Ab initio code for quasi-particle excited state energies and optical properties for solid state and molecular physics applications. |
| Software | Brief Description | |
|---|---|---|
| Avizo | GUI-based application for scientific data visualization and analysis | |
| Gephi - interactive network graph visualization | Gephi - an interactive program for network graph visualization | |
| Circos | Oriented towards genomic data display but can be applied to other data. | |
| Eye of GNOME | Image viewer (eog). | |
| Ezys - GPU-accelerated non-rigid 3D medical image registration | Ezys - GPU-accelerated non-rigid 3D medical image registration | |
| FFmpeg (video encoding) | FFmpeg - create a movie file from a series of images | |
| Gbrowse | GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. | |
| GDIS | GDIS is a scientific visualization program for the display, manipulation, and analysis of molecular and periodic structures. | |
| 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 | |
| Luscus | Luscus is a program for graphical display and editing of molecular systems. | |
| 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. | |
| MINC - Toolkit | Medical Imaging NetCDF (MINC) Toolkit | |
| Molekel | Molekel is an open-source multi-platform molecular visualization program | |
| 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. | |
| pdflib | PDF file handling library ("PDFlib-Lite" for non-commercial use). | |
| PLplot | PLplot is a cross-platform software package for creating scientific plots. | |
| Qt | Application and user interface development framework. | |
| Rasmol | Molecular graphics visualization. | |
| Vendor's OpenGL | ||
| VISAT | An image processing and data analysis program for remotely sensed data. | |
| VisIT - general purpose visualization tool | VisIT - general purpose scientific visualization tool | |
| 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 | |
|---|---|---|
| CISM | The Community Ice Sheet Model (CISM) is a next-generation ice sheet model used for predicting ice sheet evolution and sea level rise in a changing climate. | |
| CLHEP | A Class Library for High Energy Physics | |
| CompuCell3D | CompuCell3D is an open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms. | |
| GATE | GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to numerical simulations in medical imaging and radiotherapy. | |
| Geant4 | Geant4 is a toolkit for the simulation of the passage of particles through matter. | |
| ABAQUS | Comprehensive finite element modelling package | |
| ANSYS simulation software, including Fluent and CFX | ANSYS simulation software, including computational fluid dynamics packages Fluent and CFX | |
| BEAM | A toolbox for viewing and analyzing remotely-sensed data. | |
| Gadget | Simulation of cosmological structure formation. | |
| GDAL | Geospatial Data Abstraction Library. | |
| GRIB-API | GRIB-API is an API for working with GRIB meteorological data format. | |
| libLAS | ASPRS LiDAR data translation tools. | |
| Lumerical FDTD Solutions | Lumerical FDTD Solutions empowers designers to confront the most challenging photonic design problems. | |
| 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. | |
| MOM | The Modular Ocean Model (MOM) is a numerical ocean model based on the hydrostatic primitive equations. | |
| MuMax3 - Micromagnetic Simulation | MuMax3 - micromagnetic simulator | |
| 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. | |
| Seplib | A seismic data processing package from the Stanford Exploration Project (SEP). | |
| WRF | Weather Research & Forecasting Model, including WPS (WRF Pre-processing system), WRF-Chem and WRF EMS (Environmental Modeling System). |
| Software | Brief Description | |
|---|---|---|
| GNU binutils | The GNU Binutils are a collection of binary tools. | |
| Swig | SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. | |
| Allinea DDT | Powerful commercial debugger/profiler/Analyzer with useful GUI. | |
| Blitz++ | C++ template library for dense vectors and multi-dimensional arrays. | |
| Boost | An eclectic collection of C++ libraries. | |
| CLAPACK | F2C translation of LAPACK | |
| 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) | |
| dbx | Common UNIX debugger. | |
| 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 Data Language (GDL) | A tool for data analysis and visualization in such disciplines as astronomy, geosciences and medical imaging. | |
| GNU libgomp | GNU implementation of the OpenMP Application Programming Interface (API). | |
| Go | The Google Go programming language | |
| idb | Intel debugger. | |
| Jam | Make replacement for C/C++ projects. | |
| Java | Java is a programming language and computing platform. | |
| Julia | Julia is a high-level, dynamic language for technical computing | |
| LibYAML | LibYAML is a YAML 1.1 parser and emitter written in C. | |
| LIKWID - Performance analysis tools | LIKWID - Performance analysis tools for OpenMP and hybrid OpenMP/MPI programs. | |
| Lua | Lua is a powerful, fast, lightweight, embeddable scripting language. | |
| Mercurial | Distributed version control system | |
| Mono (C# environment) | Mono .NET environment to provide a platform for running C# programs. | |
| Node.JS | Node.JS asynchronous, event driven, standalone JavaScript language implementation. | |
| OCaml | OCaml: industrial strength programming language supporting functional, imperative and object-oriented styles | |
| OpenCV | ||
| Perl | Perl is a family of high-level, general-purpose, interpreted, dynamic programming languages. | |
| pgdbg | Portland Group graphical debugger. | |
| 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. | |
| RStudio | Integrated Development Environment for R | |
| Ruby | A dynamic, interpreted, open source programming language with a focus on simplicity and productivity. | |
| SCons | SCons is an Open Source software construction tool | |
| STLport | An implementation of the Standard Template Library. | |
| Subversion | An open source alternative to CVS for managing files for large development projects. | |
| tvmet | Tiny Vector Matrix library using Expression Templates. | |
| Xerces-C++ | XML parser and writer. | |
| zzFormatTest | Create/Edit/Format test, please ignore |
| Software | Brief Description | |
|---|---|---|
| Hadoop | Tool for map/reduce-style calculations | |
| parallel-netcdf | A Parallel I/O Library for NetCDF File Access | |
| 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. | |
| 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. | |
| TecIO | A library for writing data for import into Tecplot. | |
| Vim | An enhanced version of the vi text editor. |
| Software | Brief Description | |
|---|---|---|
| Lis | Lis (Library of Iterative Solvers for linear systems, pronounced [lis]) is a parallel software library for solving linear equations and eigenvalue problems that arise in the numerical solution of partial differential equations using iterative methods. | |
| 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. | |
| FEniCS | A framework for solution of differential equations by finite element methods. DOLFIN is a key component of the FEniCS environment. | |
| FETK | FETK: The Finite Element ToolKit for solving differential equations. | |
| FFTW | A widely-used FFT implementation. | |
| FreeFem++ - Partial Differential Equation Solver | FreeFem++ is typically applied to solve multiphysics non-linear systems. | |
| Gerris Flow Solver | Gerris Flow Solver - solve partial differential equations for incompressible flow | |
| GHMM | The General Hidden Markov Model library (GHMM) is a freely available C library implementing efficient data structures and algorithms for basic and extended HMMs with discrete and continous emissions. | |
| 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. | |
| Maple | Mathematical computation engine | |
| Mathematica | A comprehensive system for mathematical calculations. | |
| 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. | |
| MPFR | The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. | |
| MUMPS | Parallel direct solver for sparse systems. | |
| muParser | muParser is an extensible high performance math expression parser library written in C++. | |
| Nektar++ | Framework for partial differential equation solvers based on finite-element methods. | |
| 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. | |
| PARI/GP - computer algebra system | PARI/GP - C library and interactive shell supporting calculations in number theory. | |
| 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. | |
| scikit-learn | Scikit-Learn a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. | |
| SCOTCH | Graph and mesh partitioning, sparse matrix ordering. | |
| SGI Solver - Fast Sparse Solvers | SGISolve provides two direct solvers, PSLDLT and PSLDU, and one iterative solver, DIterative (deprecated), for sparse linear systems of equations. | |
| SLEPc | PETSc add-on eigenvalue solver for large sparse systems. | |
| SuiteSparse | a Suite of sparse matrix packages | |
| SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers) | SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers) | |
| TetGen | Tetrahedral mesh generation and 3D Delaunay triangulator. | |
| Trilinos | Object-oriented framework for linear algebra, meshing, preconditioners, solvers. |
| Software | Brief Description | |
|---|---|---|
| Singularity | Singularity is a containers solution for HPC applications | |
| 64-bit Linux CentOS | CentOS is an Enterprise-class Linux Distribution derived from sources freely provided to the public by a prominent North American Enterprise Linux vendor. | |
| 64-bit Red Hat Enterprise Linux | A Linux-based operating system developed by Red Hat and targeted towards the commercial market. | |
| 64-bit Scientific Linux | An operating system distributed by CERN that is similar to and compatible with CentOS. | |
| 64-bit SLES 11 | A Linux-based operating system designed for servers, mainframes, and workstations. | |
| bash (default) | Bash is a Unix shell. | |
| csh | The improved version of tcsh. | |
| GLOST | ||
| 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. | |
| Parallel | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. | |
| Red Hat Enterprise Linux AS | A Linux-based operating system developed by Red Hat and targeted toward the commercial market. | |
| 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 | |
|---|---|---|
| MySQL | MySQL is a popular open source database | |
| PostgreSQL | PostgreSQL is a powerful, open source object-relational database system. |