Alces Gridware Software Applications¶
This page documents the software which is currently available via the Alces Gridware project. Software applications are listed in the Alces Gridware repository with the structure
repository/type/name/version, which corresponds to:
- repository - packages are listed in the main repository if available for auto-scaling clusters, and the volatile repository otherwise.
- type - packages are listed as apps (applications), libs (shared libraries), compilers or mpi (message-passing interface API software for parallel applications)
- name - the name of the software package
- version - the published version of the software package
For example, a package listed as
main/apps/bowtie2/2.2.6 is version 2.2.6 of the Bowtie2 application, from the stable repository.
The following list is updated periodically as new software is added to the repositories. For clarity, multiple versions of the same application are not shown, unless there are significant functional differences between versions. Software categories are provided as a guide only - many packages are multi-discipline and have a range of appropriate uses.
Tools and Utilities¶
gnuplot A portable command-line driven graphing utility grace Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif idr Framework to measure the reproducibility of findings mawk mawk is an interpreter for the AWK Programming Language. parallel A shell tool for executing jobs in parallel using one or more computers
HPL A Portable Implementation of the High-Performance Linpack Benchmark for Distributed-Memory Computers memtester A userspace utility for testing the memory subsystem for faults. hpcc The HPC Challenge benchmark imb IMB is a networking benchmark tool. iozone IOzone is a filesystem benchmark tool. gpuburn GPU-Burn is a stress test for multi-GPGPU-setups. Folding@home A distributed computing project studying protein folding and misfolding
amber Set of programs for biomolecular simulation and analysis beast Cross-platform program for Bayesian MCMC analysis of molecular sequences placement An algorithm for prediction of explicit solvent atom distribution
MS Prot Tools Some hopefully useful tools for mass spectrometry applied to proteomics 454 Sequencing 454 Sequencing System Off-Instrument Software Applications suite ABRA Assembly Based ReAligner 'AbySS A de novo, parallel, paired-end sequence assembler that is designed for short reads ANGES Reconstucts ancestral genome maps from homologous markers in extant related genomes ANNOVAR Functional annotation of genetic variants from high-throughput sequencing data ARAGORN Detect tRNA genes and tmRNA genes in nucleotide sequences ArtificialFqG Ouputs artificial FASTQ files derived from a reference genome Atlas-SNP2 Next-generation sequencing suite of variant analysis tools AUGUSTUS Predicts genes in eukaryotic genomic sequences autoadapt Automatically detect and remove adaptors and primers present in a FASTQ file bam-readcount Generate metrics at single nucleotide positions BAMStats Tool to calculate and display various metrics derived from SAM/BAM files BamTools Provides a programmer's API and an end-user's toolkit for handling BAM files bamUtil Several programs that perform operations on SAM/BAM files BamView Interactive display of read alignments in BAM data files BLAST Compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches Batalign An incremental method for accurate gapped alignment BCFtools Utilities for variant calling and manipulating VCF and BCF files Bcl2FastQ A tool to handle bcl conversion and demultiplexing Bcl2FastQ A tool to handle bcl conversion and demultiplexing BCL Converter Convert *.bcl files into *_qseq.txt files BEAGLE A general purpose library for evaluating the likelihood of sequence evolution on trees BEAGLE Analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples BEAGLE A general purpose library for evaluating the likelihood of sequence evolution on trees BEDTools A flexible suite of utilities for comparing genomic features biom-format The Biological Observation Matrix (BIOM) format BIONJ An improved version of the NJ algorithm based on a simple model of sequence data BioPerl A community effort to produce Perl code which is useful in biology Biopython Set of freely available tools for biological computation written in Python bio-rainbow Package for RAD-seq related clustering and de novo assembly. Bismark A bisulfite read mapper and methylation caller BLAST (Legacy) Compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches Bowtie 2 Fast and sensitive read alignment Bowtie Ultrafast memory-efficient short read aligner BreakPointer Pinpoint rearrangement breakpoints using paired end reads CAP3 Sequence Assembly Program car Reconstructing contiguous regions of an ancestral genome cdbfasta CDB (Constant DataBase) indexing and retrieval tools for FASTA files CD-HIT A program for clustering DNA/protein sequence database at high identity with tolerance. cdhit A program for clustering and comparing protein or nucleotide sequences. CEGMA Building sets of gene annotations in eukaryotic genomes CGAT The Computational Genomics Analysis Toolkit CHANCE Assess the quality of ChiP-seq experiments CHIAMO Call genotypes from the Affymetrix 500K Mapping chip Chimerascan Detection of chimeric transcripts in high-throughput sequencing data ClonalFrame Inference of bacterial microevolution using multilocus sequence data CLUMPP Deals with label switching and multimodality problems in population-genetic cluster analyses Clustal Omega Multiple alignment of nucleic acid and protein sequences ClustalW Multiple alignment of nucleic acid and protein sequences cnD Copy number variant caller for inbred strains CNVnator CNV discovery and genotyping from depth of read mapping CoNIFER Copy Number Inference From Exome Reads CASAVA Processes sequencing reads provided by RTA or OLB CONTIGuator A bacterial genomes finishing tool for structural insights on draft genomes Control-FREEC Detect copy-number changes and allelic imbalances using deep-sequencing data CNATR Tool for copy number variation (CNV) detection for targeted resequencing data Corset Software for clustering de novo assembled transcripts and counting overlapping reads Cortex "Software for genome assembly and variation analysis CRAMTools Set of Java tools and APIs for efficient compression of sequence read data CREST Algorithm for detecting genomic structural variations at base-pair resolution CRISP Multi-sample variant caller for high-throughput pooled sequence data Curtain Assembler of next generation sequence, developed by Matthias Haimel in the Ensembl Genomes team at the EBI cutadapt A tool that removes adapter sequences from DNA sequencing reads DARWIN Data Analysis and Retrieval With Indexed Nucleotide/peptide sequences DDiMAP Analyses mapped NGS read data to discover rare variants dDocent An interactive bash wrapper to QC, assemble, map, and call SNPs from double digest RAD data Delly Structural variant discovery by integrated paired-end and split-read analysis distruct Graphically display results produced by the genetic clustering program structure DREEP Detecting low-level mutations by utilizing the RE-sequencing Error Profile of the data EAD Error aware demultiplexer is a probabilistic demultiplexer for Illumina BCL files. EIGENSOFT Combines functionality from population genetics methods and EIGENSTRAT stratification method EIGENSOFT Combines functionality from population genetics methods and EIGENSTRAT stratification method Ensembl API Abstraction layer for accessing Ensembl genomic databases Ensembl Variant Effect Predictor Predict the functional consequences of known and unknown variants e-PCR Identifies sequence tagged sites (STSs) within DNA sequences Exonerate Generic tool for pairwise sequence comparison eXpress Streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences FamSeq A computational tool for calculating probability of variants in family-based sequencing data FASTA Search protein or DNA sequence databases comparing a protein sequence to a DNA sequence database FastQC A quality control tool for high throughput sequence data fastq-tools Small utilities for working with fastq sequence files FastTree Inference of approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastUniq an ultrafast de novo duplicates removal tool for paired short DNA sequences Flexbar Flexible barcode and adapter removal for sequencing platforms FreeBayes Bayesian genetic variant detector designed to find small polymorphisms FREGENE Simulates sequence-like data over large genomic regions in large diploid populations FusionFinder Find fusion transcript candidates in RNA-Seq data FusionMap Align reads spanning fusion junctions directly to the genome Galaxy Open, web-based platform for data intensive biomedical research GBrowse The Generic Genome Browser geneid Predicts genes in anonymous genomic sequences designed with a hierarchical structure GeneTorrent Transfer genomic data reliably across a network GATK Software package developed at the Broad Institute to analyse next-generation resequencing data GAT + queue Broad Institute package for analysing next-generation resequencing data; including command-line scripting framework for defining multi-stage genomic analysis pipelines GenomeMapper Short read mapping tool designed for accurate read alignments GENSCAN Analyze genomic DNA sequences from a variety of organisms GERP++ Identifies constrained elements in multiple alignments by quantifying substitution deficits GIMSAN GIbbsMarkov with Significance ANalysis Glimmer System for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses GMAP/GSNAP Genomic mapping and alignment and short-read nucleotide alignment programs GREAT Genomic Regions Enrichment of Annotations Tool Grinder A versatile omics shotgun and amplicon sequencing read simulator GTOOL Transforms sets of genotype data for use with the programs SNPTEST and IMPUTE HAL Hierarchical Alignment Format API and analysis and conversion tools hapflk Haplotype-based test for differentiation in multiple populations HLA*IMP BE Impute HLA type information based on SNP genotypes back-end HLA*IMP FE Impute HLA type information based on SNP genotypes front-end HMMcopy Make copy number estimations for whole genome data HPCall Improved base-calling for homopolymer-sensitive next-gen data HTSeq Process data from high-throughput sequencing assays HTSlib C library for high-throughput sequencing data formats abacas Rapidly contiguate (align, order, orientate), visualize and design primers Bio-bwa Aligns relatively short nucleotide sequences against a long reference sequence such as the human genome bowtie2 Fast and sensitive read alignment bowtie Ultrafast memory-efficient short read aligner bedtools A flexible suite of utilities for comparing genomic features phast Software package for comparative and evolutionary genomics cufflinks Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples emboss Software analysis suite developed for the molecular biology community genetics Reports position-specific measures of conservation genome An alignment tool like BLAST varscan Mutation caller for targeted, exome, and whole-genome resequencing data breakdancer Provides genome-wide detection of structural variants from next generation paired-end sequencing reads Genome-music A comprehensive analysis suite for mutations in cancer genomes radmarkers Guppy RAD tools fastx A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing fastx2 Assaf Gordon text utilities hmmer Biosequence analysis using profile hidden Markov models htsfilter Standard Filter for identification of polyclonal and independant errors for SOLiD short read sequences macs Novel algorithm for identifying transcript factor binding sites sambamba Tools for working with SAM/BAM data mag Builds qassembly by mapping short reads to reference sequences picard Java-based command-line utilities and API for manipulating SAM files ribopicker Identify and remove rRNA sequences from metagenomic and metatranscriptomic datasets samtools Provides various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format plinkseq Library for working with human genetic variation data bamview Variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format recon Package for finding repeat families from biological sequences Picard-broad Command line tools for manipulating high-throughput sequencing (HTS) data and formats mabkit Tools for common BAM file manipulations speedseq A flexible framework for rapid genome analysis and interpretation fgwas Functional genomics and genome-wide association studies lighter Fast and memory-efficient sequencing error corrector bamtools3 Provides a programmer's API and an end-user's toolkit for handling BAM files diffreps Differential analysis for ChIP-seq with biological replicates Macs-taoliu Novel algorithm for identifying transcript factor binding sites sift Predicts whether an amino acid substitution affects protein function impute A genotype imputation and phasing program based on ideas from Howie et al. (2009) snpomatic Fast, stringent short-read mapping software soap A short read de novo assembly tool amos A collection of tools and class interfaces for the assembly of DNA reads bfast Facilitates the fast and accurate mapping of short reads to reference sequences kggseq A biological knowledge-based mining platform for genomic and genetic studies using sequence data passion A pattern growth algorithm based pipeline for splice site detection in paired-end RNA-Seq data Cnv-seq A method for detecting DNA copy number variation (CNV) using highthroughput sequencing tophat A spliced read mapper for RNA-Seq Tophat-fusion Enhanced version of TopHat with the ability to align reads across fusion points trinitymaseq A novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data vcftools Package designed for working with VCF files, such as those generated by the 1000 Genomes Project fastq_screen A screening application for high throughput sequence data gatk Software package developed at the Broad Institute to analyse next-generation resequencing data igv A high-performance visualization tool for interactive exploration of large, integrated genomic datasets scripture Java-based command-line tool for transcriptome reconstruction bertone Subdivision of ChIP-seq/ChIP-chip regions into discrete signal peaks oases De novo transcriptome assembler for very short reads velvet Sequence assembler for very short reads hgsc SNP discovery tool developed for next generation sequencing platforms htslib Provides various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format bam2fastq Extract raw sequences (with qualities) mothur Provides microbial ecologists with the functionality of dotur, sons, treeclimber, s-libshuff, unifrac and more. mutationtaster Next-generation sequencing pipeline from Mutation Taster (http ngsqctoolkit A toolkit for the quality control (QC) of next generation sequencing (NGS) data w.cgi Software for performing Bayesian inference Using Gibbs Sampling repeatmasker Screens DNA sequences for interspersed repeats and low complexity DNA sequences artemis Genome browser and annotation tool dindel Calls small indels from next-generation sequence data by realigning reads to candidate haplotypes reapr Evaluates the accuracy of a genome assembly using mapped paired end reads smalt Efficiently aligns DNA sequencing reads with genomic reference sequences shapeit Segmented HAPlotype Estimation and Imputation Tool - Fast and accurate haplotype inference stampy Maps short reads from Illumina sequencing machines on to a reference genome iassembler Assemble ESTs generated using Sanger and/or Roche-454 pyrosequencing technologies into contigs Infernal Search DNA sequence databases for RNA structure and sequence similarities InterProScan Allows sequences to be scanned against InterPro's signatures JAGS Analysis of Bayesian hierarchical models using Markov Chain Monte Carlo simulation Kent src utils Jim Kent and the UCSC Genome Bioinformatics Group program suite khmer k-mer counting, filtering and graph traversal LASTZ Program for aligning DNA sequences, a pairwise aligner LifeScope LifeScope Genomic Analysis Solutions Tools LOCAS Low-coverage short-read assembler LoFreq Fast and sensitive variant-caller for inferring SNVs from high-throughput sequencing data LUMPY A probabilistic framework for structural variant discovery MAFFT Multiple alignment program for amino acid or nucleotide sequences mafJoin Tool for combining pairs of maf files that share a common sequence MAKER Portable and easily configurable genome annotation pipeline M.A.Q Viewer Graphical read alignement viewer MaSuRCA Whole genome assembly Mauve Mauve Genome Alignment Software MeDUSA Methylated DNA Utility for Sequence Analysis - Computational pipeline to perform a full analysis of MeDIP-seq data MEGA Molecular Evolutionary Genetics Analysis - Software suite for analyzing DNA and protein sequence data from species and populations MEME Suite Motif-based sequence analysis tools MERLIN Uses sparse trees to represent gene flow in pedigrees Microbiome Microbiome Utilities MIRA Whole genome shotgun and EST sequence assembler MISO Probabilistic analysis and design of RNA-Seq experiments for identifying isoform regulation MitoSeek Extraction of mitochondrial genome information from exome sequencing data MODELLER Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Results mpiBLAST Open-Source Parallel BLAST MrBayes Bayesian Inference of Phylogeny Multiz/TBA Threaded-Blockset Aligner, a local multiple sequence alignment tool; MULTIZ, aligns highly rearranged or incompletely sequenced genomes MUMmer System for rapidly aligning entire genomes MUSCLE Multiple sequence alignment MuTect Reliable and accurate identification of somatic point mutations NGS-SNP Collection of command-line scripts for providing rich annotations for SNPs Novoalign Aligner for short nucleotide space reads NucleoATAC Package for calling nucleosomes using ATAC-Seq data Oases De novo transcriptome assembler for very short reads 454-OISA 454 Sequencing System Off-Instrument Software Applications suite OL Basecaller Performs base calling and bcl to qseq conversion for the HiSeq, HiScan-SQ, or Genome Analyzer ONCOCNV Detection of copy number changes in Deep Sequencing data OncoSNP-SEQ Characterise copy number alterations and loss-of-heterozygosity events Oncotator Annotate human genomic point mutations and indels with data relevant to cancer researchers OpenMS LC/MS data management and analyses PAGIT Post Assembly Genome Improvement Toolkit PAML Phylogenetic Analysis by Maximum Likelihood Panseq Determine the core and accessory regions among a collection of genomic sequences PeakRanger Multi-purporse software suite for analyzing next-generation sequencing (NGS) data PEAR PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger PeSV-Fisher Pipeline for the detection of five general types of structural variants phantompeakqual Compute quick, highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data phrap phrap is a program for assembling shotgun DNA sequence data PHYLIP A free package of programs for inferring phylogenies Pindel Detection of breakpoints of structural variants at single-based resolution from next-gen sequence data plink Whole genome association analysis toolkit Polymutt Calls single nucleotide variants and detects de novo point mutation events in families for next-generation sequencing data PolyPhen-2 Predicts possible impact of amino acid substitutions on the structure and function of human proteins popoolation2 Allows comparision of allele frequencies between two ore more populations popoolation Estimate natural variation and positive selection Preseq Predict and estimate the complexity of a genomic sequencing library Primer3 PCR primer design tool PRINSEQ Lite Filter, reformat, or trim genomic and metagenomic sequence data PROCHECK Stereochemical protein structure quality analysis ProgCactus A whole-genome alignment package PSIPRED Accurate protein secondary structure prediction PyCogent A toolkit for making sense from sequence PyNAST Python Nearest Alignment Space Termination tool pyprophet Analyse MRM data PyroBayes A novel base caller for pyrosequences from the 454 Life Sciences sequencing machines Q Whole genome association analysis toolkit Qiime Quantitative Insights Into Microbial Ecology RAxML Randomized Axelerated Maximum Likelihood Sequential and parallel inference of large phylogenies with maximum likelihood Rcount Simple and flexible RNA-Seq read counting RDP Classifier Naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus. RepeatNet An ab initio centromeric sequence detection algorithm rMATS Detect differential alternative splicing events from RNA-Seq data RMBlast NCBI Blast modified for use with RepeatMasker/RepeatModeler RSEM Estimate gene and isoform expression levels from RNA-Seq data RSeQC An RNA-seq Quality Control Package RStudio Desktop A free and open source integrated development environment for R samblaster Mark duplicates and extract discordant and split reads from sam files Satsuma High-sensitivity alignments through cross-correlation screed Short read sequence utils in Python. Scythe A very simple adapter trimmer Scythe A very simple adapter trimmer SeqAn Open source C++ library of efficient algorithms and data structures for the analysis of sequences SeqClean The Gene Indices Sequence Cleaning and Validation script (SeqClean) SeqEM Adaptive genotype-calling approach for next-generation sequencing studies SeqGene Software for mining next-gen sequencing datasets Seqtk Toolkit for processing sequences in FASTA/Q formats SRAT Programmatically access data housed within SRA and convert it from the SRA format SSAHA Sequence Search and Alignment by Hashing Algorithm - A pairwise sequence alignment program for efficient mapping of sequencing reads SVA Sequence Variant Analyzer - Annotate, visualize and analyze the genetic variants indentifed through next-generation sequencing studies SOAP Short Oligonucleotide Analysis Package - An updated version of SOAP software for short oligonucleotide alignment SHRiMP Software package for aligning genomic reads against a target genome SICER Identify enriched domains from histone modification ChIP-Seq data Sickle A windowed adaptive trimming tool for FASTQ files using quality Sickle A windowed adaptive trimming tool for FASTQ files using quality Sierra Perl Perl client to access Sierra, the Stanford HIV Web Service SiPhy Rigorous statistical tests to detect bases under selection from a multiple alignment data SNAP General purpose gene finding for both eukaryotic and prokaryotic genomes snpEff Fast variant effect predictor (SNP, MNP and InDels) for genomic data SNPTEST v2 Analysis of single SNP association in genome-wide studies SNVMix Detect single nucleotide variants from next generation sequencing data SOAPdenovoTrans A de novo transcriptome assembler designed specifically for RNA-Seq SOAPfusion Fusion discovery with paired-end RNA-Seq reads SOAP-ICLU Identify genome-wide large variants, such as CNVs and LOH etc. 'SOAPIndel' Call indels from next-generation paired-end sequencing data SOAPsnp Calls consensus genotype by carefully considering data quality, alignment and recurring experimental errors 'SOAPsplice' Genome-wide ab initio detection of splice junction sites from RNA-Seq STIR Software for Tomographic Image Reconstruction - Multi-platform object-oriented framework for data manipulations in tomographic imaging SortMeRNA SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatranscriptomic data produced by next-generation sequencers. Stacks Software pipeline for building loci from short-read sequences Staden Package A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) STAR Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays Strelka Somatic variant calling workflow for matched tumor-normal samples StructHarvester Extracting data from STRUCTURE results files Structure Use multi-locus genotype data to investigate population structure SuperHirn Tool to quantitatively analyze multi-dimensional LC-MS data SVMerge Enhanced structural variant and breakpoint detection Tabix++ C++ wrapper to Tabix indexer for TAB-delimited genome position files Tabix Generic indexer for TAB-delimited genome position files Tablet Lightweight, high-performance graphical viewer for next generation sequence assemblies and alignements Tandem Repeats Locate and display tandem repeats in DNA sequences tax2tree Assists in decorating an existing taxonomy onto a phylogenetic tree with overlapping tip names T-Coffee Align sequences or combine the output of other alignment methods into one unique alignment TMAP Torrent mapping alignment program TopHat A spliced read mapper for RNA-Seq Trans-ABySS Analyze ABySS multi-k-assembled shotgun transcriptome data treeviewx Phylogeny tree viewer Trim Galore! Wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files Trimmomatic A flexible read trimming tool for Illumina NGS data Trinity A novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data trRNAscan-SE Improved detection of transfer RNA genes in genomic sequence UNPHASED Software for genetic association analysis USeq Collection of software tools for analysis of sequencing data from the Solexa, SOLiD, and 454 platforms VariationHunter A tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies vcflib utils Command-line utilities for executing complex manipulations on VCF files Velvet Sequence assembler for very short reads VerifyBamID Verify whether reads match previously known genotypes for an individual Vienna RNA RNA Secondary Structure Prediction and Comparison Vmatch Software tool for efficiently solving large scale sequence matching tasks Wise2 Program for aligning proteins or protein HMMs to DNA WU BLAST Washington University-produced alternative to NCBI BLAST wwwblast A suite of standalone BLAST programs produced by NCBI for use on the web Bioconductor Tools for the analysis and comprehension of high-throughput genomic data
vmd Molecular visualization program for displaying, animating, and analyzing large biomolecular systems NAMD A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems
ASE Atomistic Simulation Environment - Python modules for manipulating atoms, analyzing simulations and visualization Desmond High-speed molecular dynamics simulations of biological systems DL_POLY General purpose classical molecular dynamics (MD) simulation ESPResSo Extensible Simulation Package for Research on Soft matter GAMESS General Atomic and Molecular Electronic Structure System (GAMESS) -Ab initio molecular quantum chemistry babel A chemical toolbox designed to speak the many languages of chemical data gpaw A density-functional theory (DFT) Python code gromacs Perform molecular dynamics; simulate the Newtonian equations of motion for systems with hundreds to millions of particles nwchem Methods for computing the properties of molecular and periodic systems OpenMD Open source molecular dynamics engine Maestro Schr?dinger Maestro - a powerful, all-purpose molecular modelling envirotnment
GNU GCC GNU Compiler Collection including front ends for C, C++, Objective-C and Fortran Cluster Studio Intel Cluster Studio - High performance cluster tools to increase performance and scalability Open64 An open source, optimizing compiler for the Itanium and x86-64 microprocessor architectures Oracle Java(TM) Java Programing Language
hdf5 Data model, library, and file format for storing and managing data
Octopus A scientific program aimed at the ab initio virtual experimentation
ANSYS Workbench Suite of advanced engineering simulation tools Code_Saturne Solve the Navier-Stokes equations for 2D, 2D-axisymmetric and 3D flows
GRASS GIS Free and open source Geographic Information System (GIS) software suite PROJ.4 Convert geographic longitude and latitude coordinates into cartesian coordinates
Graphics and Imaging¶
DIL Developer's Image Library - Cross-platform image library utilizing a simple syntax to load, save, convert, manipulate, filter and display a variety of images with ease POV-Ray The Persistence of Vision Raytracer vtk Package for 3D graphics, modeling and image processing Bsoft Bernard's Software Package CTFFIND3 CTF estimation CTFFIND4 CTF estimation Dynamo Software environment for subtomogram averaging of cryo-EM data EMAN2 Broadly based greyscale scientific image processing suite FFmpeg A complete, cross-platform solution to record, convert and stream audio and video IHRSR++ Extension of Iterative Helical Real Space Reconstruction (IHRSR) software IMOD Image processing, modeling and display programs for tomographic reconstruction RELION REgularised LIkelihood OptimisatioN ResMap Local Resolution Map Algorithm SPIDER System for Processing Image Data from Electron microscopy and Related fields
Anaconda Py2.7 Completely free Python distribution including popular Python packages (python 2.7) Anaconda Py3 Completely free Python distribution including popular Python packages (python 3) Cython C-Extensions for Python Glasgow Haskell Compiler and interactive environment for the functional language Haskell julia High-level, high-performance dynamic programming language for technical computing perl A highly capable, feature-rich programming language with over 24 years of development php A widely-used general-purpose scripting language that is especially suited for Web development python A remarkably powerful dynamic programming language R Language and environment for statistical computing and graphics ruby A dynamic, open source programming language with a focus on simplicity and productivity IPython Rich architecture for interactive computing Mono A software platform designed to allow developers to easily create cross platform applications Oracle Java(TM) Java Programing Language R Language and environment for statistical computing and graphics Scala Multi-paradigm programming language built on top of the Java virtual machine. Virtualenv Virtual Python Environment Builder
GCC GNU C/C++ Compiler ANTLR ANother Tool for Language Recognition - Language tool that provides a framework for constructing interpreters, compilers, and translators BLACS Basic Linear Algebra Communication Subprograms - A linear algebra oriented message passing interface Caffe A fast open framework for deep learning CUDA Toolkit Development environment for C and C++ developers building GPU-accelerated applications CythonGSL Cython interface for the GNU Scientific Library (GSL) GEOS Geometry Engine, Open Source GDAL Geospatial Data Abstraction Library Translator library for raster geospatial data formats GMP Library for arbitrary precision arithmetic GSL GNU Scientific Library - A numerical library for C and C++ programmers Rnetcdf RNetCDF libdc1394 C++ API to the PostgreSQL database management system. Math-atlas Automatically Tuned Linear Algebra Software - portably optimal linear algebra software mpi4py Python bindings for the Message Passing Interface (MPI) libgit2 Portable, pure C implementation of the Git core methods boost Free peer-reviewed portable C++ source libraries fftw C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions fltk A cross-platform C++ GUI toolkit providing modern GUI functionality without the bloat freeds A set of libraries for Unix and Linux that allow programs to natively talk to Microsoft SQL Server and Sybase databases freetype Freetype fonts package graphicsmagick Swiss army knife of image processing imagemagick An open source software suite for displaying, converting, and editing raster image files Blas-forum Reference implementation for the C interface to the Legacy BLAS blas Routines that provide standard building blocks for performing basic vector and matrix operations clapack LAPACK translated from Fortran to C lapack Linear Algebra PACKage - routines for equation solving systems scalapack A library of high-performance linear algebra routines for parallel distributed memory machines pil Adds image processing capabilities to your Python interpreter netcdf NetCDF zeroc A modern distributed computing platform. Img Support for many image formats for Tk JasPer Reference implementation of the JPEG-2000 Part-1 standard Lasagne Lightweight library to build and train neural networks in Theano libctl Flexible control files for scientific simulations libgdiplus C-based implementation of the GDI+ API Libxc Libxc is a library of exchange-correlation functionals for density-functional theory. LLVM Core A modern source- and target-independent optimizer with code generation support matplotlib 2D plotting library for Python which produces publication quality figures MPFR C library for multiple-precision floating-point computations with correct rounding NetCDF Fortran Set of interfaces and libraries for array-oriented data access NetCDF Set of interfaces and libraries for array-oriented data access numexpr Fast numerical array expression evaluator for Python and NumPy OpenBLAS An optimized BLAS library OpenCV Open source computer vision and machine learning software library OpenLibm High quality, portable, standalone C mathematical library pandas Powerful data structures for data analysis, time series,and statistics PCRE2 Perl Compatible Regular Expressions Protocol Buff Protocol Buffers are a way of encoding structured data in an efficient yet extensible format. Google uses Protocol Buffers for almost all of its internal RPC protocols and file formats. pybedtools Wrapper around BEDTools for bioinformatics work PyGTK Libraries GTK+ for Python PyQt4 Python v2 and v3 bindings for Digia's Qt application framework PyQwt PyQwt plots data with Numerical Python and PyQt Pysam Python module for reading and manipulating Samfiles PyTables Hierarchical datasets Qt A cross-platform application and UI framework QuTIP Quantum Toolbox in Python Rmpi Provides an interface (wrapper) to MPI APIs ROOT Set of OO frameworks to handle and analyze large amounts of data efficiently RPy A simple and efficient access to R from Python Seaborn Seaborn is a Python visualization library based on matplotlib. SLICOT Subroutine Library in Systems and Control Theory Snappy Java Snappy compressor/decompressor for Java SparseHash An extremely memory-efficient hash_map implementation SPIOL Staden Package I/O Libraries - I/O libraries developed as part of the Staden Project Theano Define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently TBB Threading Building Blocks - C++ template library that simplifies the development of software applications running in parallel Trilinos Algorithms for the solution of multi-physics engineering and scientific problems UDUNITS Programatic handling of units of physical quantities Ceres Solver C++ library for modeling and solving large complicated nonlinear least squares problems GetPot Tool to parse the command line and configuration files. gflags Library that implements commandline flags processing glog Application-level logging library nanoflann C++ header-only fork of FLANN, a library for KD-trees pyBigWig A python extension, written in C, for quick access to and creation of bigWig files.
eigen C++ template library for linear algebra Arpack-ng Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems numpy Fundamental package for scientific computing in Python suitesparse A suite of sparse matrix packages octave High-level interpreted language, primarily intended for numerical computations qhull General dimension code for computing convex hulls METIS Serial Graph Partitioning and Fill-reducing Matrix Ordering MGRIDGEN Obtain a sequence of successive coarse grids that are well-suited for geometric multigrid methods qrupdate Fortran library for fast updates of QR and Cholesky decompositions SciPy Scientific tools for Python SCOTCH Graph and mesh/hypergraph partitioning, graph clustering, and sparse matrix ordering SMLT The Shogun Machine Learning Toolbox - A large scale machine learning toolbox
FreeSurfer A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data FreeSurfer An open source software suite for processing and analyzing (human) brain MRI images
mvapich2 MPI-2 over OpenFabrics-IB, OpenFabrics-iWARP, PSM, uDAPL and TCP/IP mvapich MPI-1 over OpenFabrics/Gen2, OprnFabrics/Gen2-UD, uDAPL, InfiniPath, VAPI and TCP/IP mpich2 A high-performance and widely portable implementation of the MPI standard (both MPI-1 and MPI-2) MPICH A high-performance and widely portable implementation of the MPI standard (MPI-1, MPI-2 and MPI-3) Open MPI A High Performance Message Passing Library
CASTEP A leading code for calculating the properties of materials from first principles fREEDA Multi-physics simulator Harminv Extract mode frequencies from time-series data openfoam A C++ toolbox for the development of customized numerical solvers, and pre-/post-processing utilities LAMMPS Molecular Dynamics Simulator - LAMMPS ('Large-scale Atomic/Molecular Massively Parallel Simulator') is a molecular dynamics program from Sandia National Laboratories Meep Finite-difference time-domain (FDTD) simulation software MPB MIT Photonic Bands - Electromagnetic eigenmode solver
biogeme Estimation of discrete choice models
Bazel Correct, reproducible, fast builds for everyone bcrypt Cross-platform file encryption utility CMake An extensible, open-source system that manages the build process in an operating system and compiler-independent manner EC2 AMI Tools Command-line tools to create and manage Amazon Machine Images EC2 API Tools Command-line tools for managing EC2 instances Git Git - the stupid content tracker GNU Parallel Shell tool for executing jobs in parallel using one or more computers flex The fast lexical analyzer cpanminus Get, unpack, build and install modules from CPAN patchelf Utility to modify the dynamic linker and RPATH of ELF executables cmake An extensible, open-source system that manages the build process in an operating system and compiler-independent manner tau Portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python OpenStackClient Command-line client for OpenStack pip The PyPA recommended tool for installing and managing Python packages. setuptools Download, build, install, upgrade and uninstall Python packages -- easily! SIP Automatically generate Python bindings for C and C++ libraries h5utils Utilities for visualization and conversion of scientific data in HDF5 format mbuffer Tool for buffering data streams
Circos A software package for visualizing data and information. ants Advanced Normalization ToolS for brain and image mapping OctoMap A probabilistic, flexible, and compact 3D mapping library for robotic systems ParaView Data analysis and visualization