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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
Benchmarks¶
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
Biochemistry¶
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
BioInformatics¶
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
illuminautils File utilities for Illumina sequencers
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
Bio-physics¶
vmd Molecular visualization program for displaying, animating, and analyzing large biomolecular systems
molscript MolScript is a program for displaying molecular 3D structures
NAMD A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems
PyMOL PyMOL is a Python-enhanced molecular graphics tool
RasMOL RasMol is a program for molecular graphics visualisation
Chemistry¶
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 Schrodinger Maestro - a powerful, all-purpose molecular modelling environment
Compilers¶
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
Databases¶
hdf5 Data model, library, and file format for storing and managing data
Electronics¶
Octopus A scientific program aimed at the ab initio virtual experimentation
Engineering¶
ANSYS Workbench Suite of advanced engineering simulation tools
Code_Saturne Solve the Navier-Stokes equations for 2D, 2D-axisymmetric and 3D flows
Geography¶
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
Languages¶
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, supporting Project Jupyter
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
Libraries¶
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
pythonlevenshtein Python extension for computing string edit distances and similarities
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
snpsites Rapidly extract SNPs from a multi-FASTA alignment
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.
Mathematics¶
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
GCAL Computational Geometry Algorithms Library
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
Medicine¶
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
MPIs¶
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
Physics¶
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
Statistics¶
biogeme Estimation of discrete choice models
fastlowess An improved version of statsmodel's lowess
GGPlot An implementation of the grammar of graphics in R
Tools¶
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
Visualization¶
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