ModuleCategoryDescription
abinitchemABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.
afnibioAFNI (Analysis of Functional NeuroImages) is a leading software suite of C, Python, R programs and shell scripts primarily developed for the analysis and display of anatomical and functional MRI (FMRI) data. It is freely available (both in source code and in precompiled binaries) for research purposes. The software is made to run on virtually an Unix system with X11 and Motif displays. Binary Packages are provided for MacOS and Linux systems including Fedora, Ubuntu (including Ubuntu under the Windows Subsytem for Linux)
agreptoolsAGREP - approximate GREP for fast fuzzy string searching. Files are searched for a string or regular expression, with approximate matching capabilities and user-definable records.
alamodechemALAMODE is designed for analyzing lattice anharmonicity and lattice thermal conductivity of solids. By using an external DFT package such as VASP and Quantum ESPRESSO, you can extract harmonic and anharmonic force constants straightforwardly with ALAMODE. Using the anharmonic force constants, you can also calculate lattice thermal conductivity from first principles.
alphafoldOpen source code for AlphaFold
amberbioA suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active development community.
amptorchchemAMPtorch is a PyTorch implementation of the Atomistic Machine-learning Package (AMP) code that seeks to provide users with improved performance and flexibility as compared to the original code. The implementation does so by benefiting from state-of-the-art machine learning methods and techniques to be optimized in conjunction with high-throughput supercomputers. AMPtorch is built on top of PyTorch Geometric and Skorch.
anacondalangBuilt to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
angsdbioProgram for analysing NGS data.
ansyscaeANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater.
antdevelApache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.
antsdataANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data.
anviodataAnvi'o is an open-source, community-driven analysis and visualization platform for microbial 'omics. It brings together many aspects of today's cutting-edge strategies including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.
aprtoolsThe mission of the Apache Portable Runtime (APR) project is to create and maintain software libraries that provide a predictable and consistent interface to underlying platform-specific implementations.
apr-utiltoolsThe mission of the Apache Portable Runtime (APR) project is to create and maintain software libraries that provide a predictable and consistent interface to underlying platform-specific implementations.
aria2compileraria2 is a lightweight multi-protocol & multi-source, cross platform download utility operated in command-line. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink.
armadillonumlibArmadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.
arpack-ngnumlibARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
asechemThe Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
aspera-connecttoolsConnect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server.
atatchemThe Alloy-Theoretic Automated Toolkit (ATAT) is a generic name that refers to a collection of alloy theory tools
atkvisATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.
atomtoolsAtom is a hackable text editor for the 21st century, built on Electron, and based on everything we love about our favorite editors.
augustusbioAUGUSTUS is a program to find genes and their structures in one or more genomes.
autotoolsdevelThis bundle collect the standard GNU build tools: Autoconf, Automake and libtool
awscliThis package provides a unified command line interface to Amazon Web Services.
bamtoolsbioBamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
bartbioBART (Binding Analysis for Regulation of Transcription) is a bioinformatics tool for predicting functional transcription factors (TFs) that bind at genomic cis-regulatory regions to regulate gene expression in the human or mouse genomes, given a query gene set or a ChIP-seq dataset as input.
bart-mribioThe Berkeley Advanced Reconstruction Toolbox (BART) toolbox is a free and open-source image-reconstruction framework for Computational Magnetic Resonance Imaging developed by the research groups of Martin Uecker (Goettingen University), Jon Tamir (UT Austin), and Michael Lustig (UC Berkeley). It consists of a programming library and a toolbox of command-line programs. The library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms. The command-line tools provide direct access to basic operations on multi-dimensional arrays as well as efficient implementations of many calibration and reconstruction algorithms for parallel imaging and compressed sen.
bbmapbioBBMap includes a short read aligner, and other bioinformatic tools.
bcftoolsbioBCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF
beaglebioBeagle is a software package for phasing genotypes and for imputing ungenotyped markers.
bedopsbioBEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.
bedtoolsbioThe BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.
berkeley_dbtoolsBerkeley DB is a family of embedded key-value database libraries providing scalable high-performance data management services to applications.
berkeleygwThe BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules.
bicseq2-normbioBICseq2 is an algorithm developed for the normalization of high-throughput sequencing (HTS) data and detect copy number variations (CNV) in the genome. BICseq2 can be used for detecting CNVs with or without a control genome. BICseq2-norm is for normalizing potential biases in the sequencing data.
bicseq2-segbioBICseq2 is an algorithm developed for the normalization of high-throughput sequencing (HTS) data and detect copy number variations (CNV) in the genome. BICseq2 can be used for detecting CNVs with or without a control genome. BICseq2-seg is for detecting CNVs based on the normalized data given by BICseq2-norm.
bioawkbioBioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and an command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.
biocondabioBioconda is a channel for the conda package manager specializing in bioinformatics software.
bioperlbioBioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects.
biopythonbioBiopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
bismarkbioA tool to map bisulfite converted sequence reads and determine cytosine methylation states
bisonlangBison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
blastbioBasic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
blatbioBLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
blendervisBlender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.
blitz++libBlitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an object-oriented interface
boostdevelBoost provides free peer-reviewed portable C++ source libraries.
bowtie2bioBowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
bsmapbioBSMAP is a short reads mapping program for bisulfite sequencing in DNA methylation study. Bisulfite treatment coupled with next generation sequencing could estimate the methylation ratio of every single Cytosine location in the genome by mapping high throughput bisulfite reads to the reference sequences.
bwabioBurrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
bzip2toolsbzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
caffe2libCaffe is a deep learning framework made with expression, speed, and modularity in mind
cairovisCairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB
canubioCanu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing
caviarbiocaviar is a statistical framework that quantifies the probability of each variant to be causal while allowing with arbitrary number of causal variants.
cc3dvisCompuCell3D is a flexible scriptable modeling environment, which allows the rapid construction of sharable Virtual Tissue in silico simulations of a wide variety of multi-scale, multi-cellular problems including angiogenesis, bacterial colonies, cancer, developmental biology, evolution, the immune system, tissue engineering, toxicology and even non-cellular soft materials. CompuCell3D models have been used to solve basic biological problems, to develop medical therapies, to assess modes of action of toxicants and to design engineered tissues. CompuCell3D's intuitive interface makes Virtual Tissue modeling accessible to users without extensive software development or programming experience.
cd-hitbioCD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
cellassigncellassign automatically assigns single-cell RNA-seq data to known cell types across thousands of cells accounting for patient and batch specific effects. Information about a priori known markers cell types is provided as input to the model in the form of a (binary) marker gene by cell-type matrix. cellassign then probabilistically assigns each cell to a cell type, removing subjective biases from typical unsupervised clustering workflows.
cellprofilerbioCellProfiler is an image processing package to generate morphometric measurements.
cellrangerA set of analysis piplines that perform sample demultiplexing, barcode processing, and single cell 3' gene counting.
cellranger-arcCell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage.
cellranger-atacbioCell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.
cellranger-dnabioCell Ranger DNA is a set of analysis pipelines that process Chromium single cell DNA sequencing output to align reads, identify copy number variation (CNV), and compare heterogeneity among cells.
cesmgeoCESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states.
cgalThe goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library.
chemps2chemCheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry.
circosbioCircos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.
clapackmathC version of LAPACK
clearcutbioClearcut is the reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm by J. Evans, L. Sheneman, and J. Foster from the Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.
clhepnumlibThe CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package.
cloudcomparevisCloudCompare is a 3D point cloud (and triangular mesh) processing software. It has been originally designed to perform comparison between two dense 3D points clouds (such as the ones acquired with a laser scanner) or between a point cloud and a triangular mesh.
cmakedevelCMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
cnnpeaksbioCNN-peaks is a Convolution Neural Network(CNN) based ChIP-Seq peak calling software.
code-servertoolsRun VS Code on any machine anywhere and access it in the browser.
codeblockslangCode::Blocks is a free C, C++ and Fortran IDE built to meet the most demanding needs of its users. It is designed to be very extensible and fully configurable.
cp-analystbioCellProfiler Analyst (CPA) allows interactive exploration and analysis of data, particularly from high-throughput, image-based experiments. Included is a supervised machine learning system which can be trained to recognize complicated and subtle phenotypes, for automatic scoring of millions of cells. CellProfiler is an image processing package to generate morphometric measurements.
cp2kchemCP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.
cppchecktoolsCppcheck is a static analysis tool for C/C++ code. It provides unique code analysis to detect bugs and focuses on detecting undefined behaviour and dangerous coding constructs.
cromwelltoolsCromwell is a Workflow Management System geared towards scientific workflows.
crossftpCrossFTP is a free FTP, SFTP, WebDav, Amazon S3, Amazon Glacier, Microsoft Azure, Google storage, and OpenStack Swift client for Win, Mac, and Linux.
cudasystemCUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
cudatoolkittoolsThe NVIDIA CUDA Toolkit provides a development environment for creating high performance GPU-accelerated applications. With the CUDA Toolkit, you can develop, optimize and deploy your applications on GPU- accelerated embedded systems, desktop workstations, enterprise data centers, cloud-based platforms and HPC supercomputers. The toolkit includes GPU-accelerated libraries, debugging and optimization tools, a C/C++ compiler and a runtime library to deploy your application.
cudnnnumlibThe NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
cufflinksCufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
cumulus_feature_barcodingA fast C++ tool to extract feature-count matrix from sequence reads in FASTQ files. We uses isal-l for decompressing and Heng Li's kseq library for read parsing. It is used by Cumulus for feature-count matrix generation of cell hashing, nucleus hashing, CITE-Seq and Perturb-seq protocols, using either 10x Genomics V2 or V3 chemistry.
curltoolslibcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.
cutadaptbioCutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cytoscapetoolsCytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.
danposbioA toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2.
dddvisDDD is a graphical front-end for command-line debuggers such as GDB, DBX, WDB, Ladebug, JDB, XDB, the Perl debugger, the bash debugger bashdb, the GNU Make debugger remake, or the Python debugger pydb.
decontaminerbiodecontaMiner, a tool for detecting contaminating organisms in human unmapped sequences.
deeplabcutDeepLabCut is a toolbox for markerless pose estimation of animals performing various tasks.
deeptoolsbiodeepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.
diamondbioDIAMOND is a sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000.
doxygendevelDoxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.
dragonndataThe dragonn package implements Deep RegulAtory GenOmic Neural Networks (DragoNNs) for predictive modeling of regulatory genomics, nucleotide-resolution feature discovery, and simulations for systematic development and benchmarking.
drmaatoolsDRMAA for Slurm Workload Manager (Slurm) is an implementation of Open Grid Forum Distributed Resource Management Application API (DRMAA) version 1 for submission and control of jobs to Slurm. Using DRMAA, grid applications builders, portal developers and ISVs can use the same high-level API to link their software with different cluster/resource management systems.
eccodesecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).
eclipsetoolsEclipse provides IDEs and platforms for many programming languages. This module includes Java support.
eigenEigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
eigensoftbioThe EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.
elpaEigenvalue SoLvers for Petaflop-Applications .
embossbioEMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
epactstoolsEPACTS (Efficient and Parallelizable Association Container Toolbox) is a versatile software pipeline to perform various statistical tests for identifying genome-wide association from sequence data through a user-friendly interface, both to scientific analysts and to method developers.
epicbioepic is a software package for finding medium to diffusely enriched domains in chip-seq data. It is a fast, parallel and memory-efficient implementation of the popular SICER algorithm.
epstopdftoolsEpstopdf is a Perl script that converts an EPS file to an ‘encapsulated’ PDF file (a single page file whose media box is the same as the original EPS’s bounding box).
esmfgeoThe Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models.
evmbioThe EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.
exoneratebioExonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.
fastabioThe FASTA programs find regions of local or global (new) similarity between protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.
fastenlocbiofastENLOC: fast enrichment estimation aided colocalization analysis enables integrative genetic association analysis of molecular QTL data and GWAS data.
fastqcbioFastQC is a Java application which takes a FastQ file and runs a series of tests on it to generate a comprehensive QC report.
fastqtlbioFastQTL is a QTL mapper
fastx-toolkitbioThe FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
febiocaeFEBio is a nonlinear finite element solver that is specifically designed for biomechanics and biophysics applications.
ffmpegvisA complete, cross-platform solution to record, convert and stream audio and video.
fftwnumlibFFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
fgslnumlibFGSL: A Fortran interface to the GNU Scientific Library
fgwaslibfgwas is a command line tool for integrating functional genomic information into a genome-wide association study (GWAS).
fijitoolsFiji is an image processing distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
finestructurebiofineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data.
fltkvisFLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.
fortrangisgeoFortranGIS project includes a collection of Fortran interfaces to some common Open Source GIS (Geographic Information System) software libraries, plus some more Fortran-specific tools.
freebayesbioFreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
freesurferbioFreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data.
freexllibFreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet.
fribidilangThe Free Implementation of the Unicode Bidirectional Algorithm.
fsabioFSA:Fast Statistical Alignment, is a probabilistic multiple sequence alignment algorithm which uses a distance-based approach to aligning homologous protein, RNA or DNA sequences.
fslbioFSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
funannotatebioFunannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this software package was to be able to accurately and easily annotate a genome for submission to NCBI GenBank. Existing tools (such as Maker) require significant manually editing to comply with GenBank submission rules, thus funannotate is aimed at simplifying the genome submission process.
gatkThe Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
gaussianchemGaussian is a suite of electronic-structure codes.
gawkThe awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code.
gcccompilerThe GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
gcccudatoolchainGNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.
gcloud-sdktoolsThe Cloud SDK is a set of tools for Cloud Platform. It contains gcloud, gsutil, and bq, which you can use to access Google Compute Engine, Google Cloud Storage, Google BigQuery, and other products and services from the command-line.
gdbioGD.pm - Interface to Gd Graphics Library
gdaldataGDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.
gdal-grassdataThe idea of the GDAL-GRASS plugin is to directly access GRASS raster and vector data from outside. Any GDAL enabled software (QGIS, R, ...) can read and write through the plugin from the GRASS database.
gdbdebuggerThe GNU Project Debugger
gdc-clienttoolsThe gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS.
geanytoolsGeany is a text editor using the GTK+ toolkit with basic features of an integrated development environment.
gemmabioGenome-wide Efficient Mixed Model Association
genometoolsbioThe GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.
genrichbioGenrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.
geosmathGEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
gffcomparebioThe program gffcompare can be used to compare, merge, annotate, and estimate accuracy of one or more GFF files (the 'query' files), when compared with a reference annotation (also provided as GFF).
gftptoolsgFTP is a free multithreaded file transfer client for *NIX based machines.
ghostscripttoolsGhostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.
gittoolsGit is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
git-lfstoolsGit Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com
gladevisGlade is a RAD tool to enable quick & easy development of user interfaces for the GTK+ toolkit and the GNOME desktop environment.
glewlibThe OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform.
glfwlibGLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop. It provides a simple API for creating windows, contexts and surfaces, receiving input and events.
globus_clitoolsGlobus CLI is a standalone application that can be installed on the user’s machine and used to access the Globus file transfer service.
gmap-gsnapbioGMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program
gmpmathGMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
gnupgtoolsGnuPG is a complete and free implementation of the OpenPGP standard as defined by RFC4880 (also known as PGP). GnuPG allows you to encrypt and sign your data and communications; it features a versatile key management system, along with access modules for all kinds of public key directories.
gnuplotvisPortable interactive, function plotting utility
golangGo is an open source programming language that makes it easy to build simple, reliable, and efficient software.
gobject-introspectiondevelGObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.
gofficelibGOffice is a GObject based C library. It provides easy API access to creating and manipulating graphs and canvases.
gompitoolchainGNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support.
gompictoolchainGNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.
google-apitoolsGoogle APIs give you programmatic access to Google Maps, Google Drive, YouTube, and many other Google products.
goolftoolchainGNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
goolfctoolchainGNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK with CUDA features enabled.
gparalleltoolsGNU parallel is a shell tool for executing jobs in parallel using one or more computers.
gperfbaseNone
gperftoolstoolsgperftools are for use by developers so that they can create more robust applications. Especially of use to those developing multi-threaded applications in C++ with templates. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler.
gpunufftdataGPU Regridding of arbitrary 3-D/2-D MRI data
gpustattoolsdstat-like utilization monitor for NVIDIA GPUs
gracevisGrace is a WYSIWYG 2D plotting tool for X Windows System and Motif.
grassgeoThe Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization
grib_apidataThe ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of command line tools is also provided to give quick access to GRIB messages.
gromacschemGROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
gslThe GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
gtk+visThe GTK+ 3 package contains libraries used for creating graphical user interfaces for applications.
gurobimathThe Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms.
gziptoolsgzip (GNU zip) is a popular data compression program as a replacement for compress
hapflowbioHapFlow is a python application for visualising haplotypes present in sequencing data. It identifies variant profiles present and reads and creates an abstract visual representation of these profiles to make haplotypes easier to identify.
hdfHDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines.
hdf-eosdataThe HDF-EOS2 is a software library designed built on HDF4* to support EOS-specific data structures, namely Grid, Point, and Swath.
hdf5HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.
hexrdphysHEXRD provides a collection of resources for analysis of x-ray diffraction data, especially high-energy x-ray diffraction. HEXRD is comprised of a library and API for writing scripts, a command line interface, and an interactive graphical user interface.
hic-probioHiC-Pro is an optimized and flexible pipeline for Hi-C data processing.
hisat2bioHISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).
homertoolsHOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data.
hoomdchemHOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs.
htslibbioA C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
hydratordataHydrator converts Twitter IDs into JSON files.
hyprenumlibHypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.
iculibICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
idlIDL is an interpreted programming language used to create analyses and visualizations of numerical data.
idrbioThe IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility. The IDR method compares a pair of ranked lists of identifications (such as ChIP-seq peaks).
igvtoolsThis package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline.
iintelmpitoolchainIntel C/C++ and Fortran compilers with IntelMPI.
imagemagickvisImageMagick is a software suite to create, edit, compose, or convert bitmap images
impute2bioIMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009
inkscapelibInkscape is a free and open source professional vector graphics editor.
intelcompilerIntel C and C++ compilers
intelmpimpiIntelMPI from Intel.
intervenebioIntervene is a tool for intersection and visualization of multiple genomic region sets.
intltoollangThe Intltool is an internationalization tool used for extracting translatable strings from source files, collecting the extracted strings with messages from traditional source files, and merging the translations into .xml, .desktop and .oaf files.
io_libbioIo_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows.
iqtreebioEfficient phylogenomic software by maximum likelihood
irfinderbioIRFinder is a tool for detecting intron retention from RNA-Seq experiments.
isaacgymNVIDIA’s physics simulation environment for reinforcement learning research.
isoseqenvbioIsoDeq3 is a Scalable De Novo Isoform Discovery
jagsmathJAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
jaspervisThe JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
javalangJava Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
jcudabioJava bindings for NVIDIA CUDA and related libraries.
jellyfishJellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
jqtoolsjq is a lightweight and flexible command-line JSON processor.
jtreeviewvisTreeView is an open-source Java app for visualizing large data matrices. It can load a dataset, cluster it, browse it, customize its appearance and export it (or parts of it) into a figure.
juicerbioJuicer is a one-click pipeline for processing terabase scale Hi-C datasets.
julialangJulia is a high-level, high-performance dynamic programming language for numerical computing. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and an extensive mathematical function library.
junitdevelA programmer-oriented testing framework for Java.
kallistobioKallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
kim-apichemOpen Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all.
knimedataKNIME is an analytics platform for data mining.
krakenbioKraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
kraken2Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.
lamedataLAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
lammpschemLAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
lapacknumlibLAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.
ledalibRStudio is a set of integrated tools designed to help you be more productive with R. LEDA is a C++ class library for efficient data types and algorithms that provide algorithmic in-depth knowledge of graph- and network problems, geometric computations, combinatorial opimization and other.
leptonicavisLeptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications.
levmarnumlibLevmar is an implementation of Levenberg-Marquardt in C
lftptoolslftp is a sophisticated file transfer program supporting a number of network protocols.
lhapdfphysLHAPDF is a general purpose C++ interpolator, used for evaluating PDFs from discretised data files.
libfabriclibLibfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric.
libgdlibGD is an open source code library for the dynamic creation of images by programmers.
libgeotifflibLibrary for reading and writing coordinate system information from/to GeoTIFF files
libgladelibLibglade is a library for constructing user interfaces dynamically from XML descriptions.
libgsfliblibgsf -- The G Structured File Library aims to provide an efficient extensible i/o abstraction for dealing with different structured file formats.
libharuliblibHaru is a free, cross platform, open source library for generating PDF files.
libibmadsystemlibibmad is a convenience library to encode, decode, and dump IB MAD packets. It is implemented on top of and in conjunction with libibumad (the umad kernel interface library.)
libibumadsystemlibibumad is the umad kernel interface library.
libintchemLibint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.
libmathevallibGNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.
librmathlibThe routines supporting the distribution and special functions in R and a few others are declared in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications.
librsvgvislibrsvg is a library to render SVG files using cairo.
libsndfilelibLibsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.
libspatialitelibSpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities.
libxsmmmathLIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).
libyamllibLibYAML is a YAML parser and emitter written in C.
lightgbmdataLightGBM is a gradient boosting framework that uses tree based learning algorithms.
llvmcompilerThe LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.
locuszoombioLocusZoom Standalone is for the command line (standalone) version of LocusZoom, an application for creating regional plots from genome-wide association studies built in Python and R.
longrangerbioLong Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants.
macs2bioMACS (Model-based Analysis of ChIP-Seq) identifies transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of binding sites through combining the information of both sequencing tag position and orientation.
maestrobioMAESTRO(Model-based AnalysEs of Single-cell Transcriptome and RegulOme) is a comprehensive single-cell RNA-seq and ATAC-seq analysis suit built using snakemake. MAESTRO combines several dozen tools and packages to create an integrative pipeline, which enables scRNA-seq and scATAC-seq analysis from raw sequencing data (fastq files) all the way through alignment, quality control, cell filtering, normalization, unsupervised clustering, differential expression and peak calling, celltype annotation and transcription regulation analysis.
mafftbioMAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
mantabioManta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.
margebioMARGE is a robust methodology that leverages a comprehensive library of genome-wide H3K27ac ChIP-seq profiles to predict key regulated genes and cis-regulatory regions in human or mouse.
mathematica
matlab
mavendevelBinary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information.
mayavivisA tool for easy and interactive visualization of data.
mcrmathThe MATLAB Runtime 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.
memeThe MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo.
mesontoolsMeson is a cross-platform build system designed to be both as fast and as user friendly as possible.
metamorpheusMetaMorpheus is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability. This program combines features of Morpheus and G-PTM-D in a single tool.
metismathMETIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
micromambaMicromamba is a small, pure-C++ executable with enough functionalities to bootstrap fully functional conda-environments.
mirdeep2biomiRDeep2 discovers active known or novel miRNAs from deep sequencing data (Solexa/Illumina, 454, ...).
moisttoolsmoist is a Python database adaptor for MySQL, MariaDB, and (eventually) Drizzle. It is a continuation of the development fork of MySQLdb, i.e. pre-2.0.
mongoshtoolsThe MongoDB Shell, mongosh, is a fully functional JavaScript and Node.js 14.x REPL environment for interacting with MongoDB deployments. You can use the MongoDB Shell to test queries and operations directly with your database.
mothurbioMothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
mpfrmathThe MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
mrtrix3bioMRtrix3 provides a set of tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses. It is designed with consistency, performance, and stability in mind, and is freely available under an open-source license. It is developed and maintained by a team of experts in the field, fostering an active community of users from diverse backgrounds.
mrtrix3tissuebioMRtrix3Tissue is a fork of the MRtrix3 project. It aims to add capabilities for 3-Tissue CSD modelling and analysis to a complete version of the MRtrix3 software.
multiqcbioMultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
mumax3toolsGPU accelerated micromagnetic simulator.
mummerbioMUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.
musclebioMUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes—only a handful of command-line options are needed to perform common alignment tasks.
mutectbioMuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.
mutsigcvbioMutSig stands for "Mutation Significance". MutSig analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.
mysqlclientlibPython interface to MySQL
namdchemNAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
nanopolishbioSoftware package for signal-level analysis of Oxford Nanopore sequencing data.
nasmlangNASM: General-purpose x86 assembler
ncbi-vdbbioThe SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
nccllibThe NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.
ncdutoolsNcdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like environment with ncurses installed.
ncldataNCL is an interpreted language designed specifically for scientific data analysis and visualization.
ncursesdevelThe Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.
ncviewvisNcview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc.
netcdfdataNetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. This module bundles the C++ and Fortran libaries.
netlogomathNetLogo is a multi-agent programmable modeling environment. It is used by tens of thousands of students, teachers and researchers worldwide. It also powers HubNet participatory simulations. It is authored by Uri Wilensky and developed at the CCL.
netperfbaseNone
neuronbioEmpirically-based simulations of neurons and networks of neurons.
nextflowtoolsNextflow is a reactive workflow framework and a programming DSL that eases the writing of computational pipelines with complex data.
ngsbioNGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.
ngsfbiongsF is a program to estimate per-individual inbreeding coefficients under a probabilistic framework that takes the uncertainty of genotype's assignation into account. It avoids calling genotypes by using genotype likelihoods or posterior probabilities.
ninjatoolsNinja is a small build system with a focus on speed.
nodejslangNode.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices.
nsegbioNseg is used to identify low complexity sequencesi.
ntlmathNTL is a high-performance, portable C++ library providing data structures and algorithms for manipulating signed, arbitrary length integers, and for vectors, matrices, and polynomials over the integers and over finite fields.
numactltoolsThe numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.
nvhpccompilerC, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)
nvompicNVHPC Compiler including OpenMPI for MPI support.
ocamlcompilerOCaml is an industrial-strength programming language supporting functional, imperative and object-oriented styles
ocp-modelsocp-models is the modeling codebase for the Open Catalyst Project. It provides implementations of state-of-the-art ML algorithms for catalysis that take arbitrary chemical structures as input to predict energy / forces / positions
openbabelchemOpen Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
openblasnumlibOpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
openbugsmathOpenBUGS is a software application for the Bayesian analysis of complex statistical models using Markov chain Monte Carlo (MCMC) methods.
openfoamOpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.
openjpeglibOpenJPEG is an open-source JPEG 2000 codec written in C.
openmmchemOpenMM is a toolkit for molecular simulation using high performance GPU code.
openmpiThe Open MPI Project is an open source MPI-3 implementation.
openmsbioOpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software.
openslidebioOpenSlide is a C library that provides a simple interface to read whole-slide images.
openslide-pythonvisPython bindings for the OpenSlide libary
openspeedshoptool
orcachemORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
p3dfftnumlibP3DFFT is a library for large-scale computer simulations on parallel platforms.
p4vaspchemVariation graphs provide a succinct encoding of the sequences of many genomes.
p7ziptoolsp7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.
paintorbioPAINTOR is a statistical fine-mapping method that integrates functional genomic data with association strength from potentially multiple populations (or traits) to prioritize variants for follow-up analysis.
pandocIf you need to convert files from one markup format into another, pandoc is your swiss-army knife
paralleltoolsparallel: Build and execute shell commands in parallel
paraviewvisParaView is a scientific parallel visualizer.
parmetisnumlibParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.
pasapipelinelibPASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation consistent with the most recently available experimental sequence data. PASA also identifies and classifies all splicing variations supported by the transcript alignments.
patricbioPATRIC is an integration of different types of data and software tools that support research on bacterial pathogens.
pbwtbioThe pbwt package provides a core implementation and development environment for PBWT (Positional Burrows-Wheeler Transform) methods for storing and computing on genome variation data sets.
pcmsolverchemAn API for the Polarizable Continuum Model.
pcre2develThe PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
peakseqbioPeakSeq is a program for identifying and ranking peak regions in ChIP-Seq experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from a control experiment and outputs a file with peak regions ranked with increasing Q-values.
peerbioPEER is a collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods.
perftoolsPerformance analysis tools for Linux
perllangLarry Wall's Practical Extraction and Report Language
petscnumlibPETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
pgicompilerC, C++ and Fortran compilers from The Portland Group - PGI
phonopychemPhonopy is an open source package of phonon calculations based on the supercell approach. Phono3py calculates phonon-phonon interaction and related properties using the supercell approach.
picardbioA set of tools (in Java) for working with next generation sequencing data in the BAM format.
pigztoolspigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries.
pipenvtoolsPipenv is a tool that aims to bring the best of all packaging worlds (bundler, composer, npm, cargo, yarn, etc.) to the Python world.
platform-mpimpiPlatform MPI is an MPI-2 implementation from IBM.
plinkbioPLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.
plumedchemPLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
pnetcdfdataParallel netCDF: A Parallel I/O Library for NetCDF File Access
pompitoolchainToolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI.
popplervisPoppler is a PDF rendering library based on the xpdf-3.0 code base.
postgresqldataPostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.
pov-rayvisThe Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports.
projlibProgram proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
prokkabioProkka is a software tool for the rapid annotation of prokaryotic genomes.
proteowizbioProteoWizard provides a set of open-source, cross-platform software libraries and tools (e.g. msconvert, Skyline, IDPicker, SeeMS) that facilitate proteomics data analysis. The libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations.
psipredThe PSIPRED Workbench provides a range of protein structure prediction methods.
pslibtoolspslib is a C-library to create PostScript files on the fly. It offers many drawing primitives, inclusion of png and eps images and a very sophisticated text rendering including hyphenation, kerning and ligatures.
psmcbioPSMC infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model.
pybind11libpybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code.
pycairovisPython bindings for the cairo library
pygobjectvisPython Bindings for GLib/GObject/GIO/GTK+
pygtkvisPyGTK lets you to easily create programs with a graphical user interface using the Python programming language.
pyopenglvisPyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.
pythonlangPython is a programming language that lets you work more effectively.
pytorchdataPyTorch is a deep learning framework that puts Python first. It provides Tensors and Dynamic neural networks in Python with strong GPU acceleration.
pyyamllibPyYAML is a YAML parser and emitter for the Python programming language.
qiimebioQIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
qiime2bioQIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.
qt5develQt is a comprehensive cross-platform C++ application framework.
qt5webkitQt Port of WebKit. WebKit is an open source web browser engine.
qtltoolsbioQTLtools is a tool set for molecular QTL discovery and analysis. It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps.
qualimapbioQualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
quantumespressochemQuantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).
qwtlibThe Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background.
rapidsaidataThe RAPIDS suite of open source software libraries and APIs gives you the ability to execute end-to-end data science and analytics pipelines entirely on GPUs. Licensed under Apache 2.0, RAPIDS is incubated by NVIDIA based on extensive hardware and data science science experience. RAPIDS utilizes NVIDIA CUDA primitives for low-level compute optimization, and exposes GPU parallelism and high-bandwidth memory speed through user-friendly Python interfaces.
rasqualbioRASQUAL (Robust Allele Specific QUAntification and quality controL) maps QTLs for sequenced based cellular traits by combining population and allele-specific signals.
raxmlbioRAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
rclonetoolsRclone ("rsync for cloud storage") is a command line program to sync files and directories to and from different cloud storage providers.
rdp-classifierbioThe RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.
readosmlibReadOSM is an open source library to extract valid data from within an Open Street Map input file.
redis-cliRedis is an open source (BSD licensed), in-memory data structure store, used as a database, cache, and message broker.
reframesystemReFrame Regression Testing Suite
relionbioRELION (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).
remoratoolsREsource MOnitoring for Remote Applications
repast_hpclangRepast for High Performance Computing (Repast HPC) is a next generation agent-based modeling system intended for large-scale distributed computing platforms.
rip-mdbioRIP-MD allows to apply Residue Interaction Networks (RINs) to the analysis of molecular dynamics simulations of protein.
rmats-turbobiorMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.sourceforge.net). The major difference between rMATS turbo and rMATS is speed and space usage. rMATS turbo is 100 times faster and the output file is 1000 times smaller than rMATS. These advantages make analysis and storage of a large scale dataset easy and convenient.
rosettabioThe Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.
rsembioRNA-Seq by Expectation-Maximization
rstudioRStudio is a set of integrated tools designed to help you be more productive with R.
rubylangRuby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
rustlangRust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
sagemathdataSageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers.
saintSignificance Analysis of INTeractome (SAINT) consists of a series of software tools for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.
saintexpressSignificance Analysis of INTeractome (SAINT) consists of a series of software tools for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.
salmonbioSalmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.
sambambaSambamba is a tool for processing BAM files.
samtoolsbioSAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
sasmathStatistical analysis package
sbtA build tool for Scala.
scalapacknumlibThe ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
sconsdevelSCons is a software construction tool.
scotchmathSoftware package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
sdl2libSDL: Simple DirectMedia Layer, a cross-platform multimedia library
seacrbioSEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes (i.e. regions with no read coverage).
seqoutbiasbioMolecular biology enzymes have nucleic acid preferences for their substrates; the preference of an enzyme is typically dictated by the sequence at or near the active site of the enzyme. This bias may result in spurious read count patterns when used to interpret high-resolution molecular genomics data. The seqOutBias program aims to correct this issue by scaling the aligned read counts by the ratio of genome-wide observed read counts to the expected sequence based counts for each k-mer.
sgabioSGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads.
sgpdataGossip-based distributed optimization algorithms implemented in PyTorch
shapeitbioSHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.
shapeit4bioSHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data. The version 4 is a refactored and improved version of the SHAPEIT algorithm.
shapeliblibThe Shapefile C Library provides the ability to write simple C programs for reading, writing and updating (to a limited extent) ESRI Shapefiles, and the associated attribute file (.dbf).
shengbteShengBTE is a software package for solving the Boltzmann Transport Equation for phonons.
sibil-envvisThis module sets up the environment for the SIBIL application.
sicerpybioSICER.py is a Python wrapper for the SICER peak caller software.
siestaSIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
silodataSilo is a library for reading and writing a wide variety of scientific data to binary, disk files
singularitycontainersystemSingularity enables users to have full control of their environment. Singularity containers can be used to package entire scientific workflows, software and libraries, and even data.
skopeotoolsskopeo is a command line utility that performs various operations on container images and image repositories.
slatecFortran 77 numerical library.
slepcnumlibSLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.
slicertools3D Slicer is an open source software platform for medical image informatics, image processing, and three-dimensional visualization.
slimbioSLiM is an evolutionary simulation package that provides facilities for very easily and quickly constructing genetically explicit individual-based evolutionary models.
smrtlinkPacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided
snakemaketoolsThe Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
snapSNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.
snap-stanfordvisSnap.py is a Python interface for SNAP. SNAP is a general purpose, high performance system for analysis and manipulation of large networks. SNAP is written in C++ and optimized for maximum performance and compact graph representation. It easily scales to massive networks with hundreds of millions of nodes, and billions of edges.
sortmernabioSortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads.
spackSpack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine.
spadesbioSPAdes - St. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines.
sparkdevelSpark is Hadoop MapReduce done in memory
sparseassemblerbioA sparse graph approach to de novo genome assembly
sparsehashAn extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed.
spglibSpglib is a library for finding and handling crystal symmetries written in C.
sprnglibScalable Parallel Pseudo Random Number Generators Library
sqliteSQLite: SQL Database Engine in a C Library
sratoolkitbioThe SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format
stacksbioStacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
starbioSTAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
statamathStata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics.
stringtiebioStringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
subversiontoolsSubversion is an open source version control system.
suitesparsenumlibSuiteSparse is a collection of libraries manipulate sparse matrices.
sundialsmathSUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
superlunumlibSuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations.
superlu_mtSuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations.
swigSWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
tabixbioGeneric indexer for TAB-delimited genome position files
taggraphbioTagGraph is a computational tool that provides an unrestricted string-based search method that is as much as 350-fold faster than existing approaches, and a probabilistic validation model that was optimized for post-translational modification assignments.
tbblibIntel(R) Threading Building Blocks (Intel(R) TBB) makes parallel performance and scalability accessible to software developers who are writing loop- and task-based applications. Build robust applications that abstract platform details and threading mechanisms while achieving performance that scales with increasing core count.
tensorflowTensorFlow is an open-source software library for Machine Intelligence.
tesseractvisTesseract is an optical character recognition engine
texinfodevelTexinfo is the official documentation format of the GNU project.
texlivetoolsTeX Live is intended to be a straightforward way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, macOS, and also Windows. It includes all the major TeX-related programs, macro packages, and fonts that are free software, including support for many languages around the world.
thermorawfileparserbioWrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono (works on Windows too).
thirdorderchemPython package for creating input for ShengBTE.
tmuxtoolstmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.
tophatbioTopHat is a fast splice junction mapper for RNA-Seq reads.
torusbioTORUS - QTL Discovery utilizing Genomic Annotations is a free software package that implements a computational procedure for discovering molecular QTLs incorporating genomic annotations.
totalviewdebuggerTotalView is a GUI-based source code defect analysis tool that gives you unprecedented control over processes and thread execution and visibility into program state and variables. It allows you to debug one or many processes and/or threads in a single window with complete control over program execution. This allows you to set breakpoints, stepping line by line through the code on a single thread, or with coordinated groups of processes or threads, and run or halt arbitrary sets of processes or threads. You can reproduce and troubleshoot difficult problems that can occur in concurrent programs that take advantage of threads, OpenMP, MPI, GPUs or coprocessors.
treetoolsTree is a recursive directory listing command that produces a depth indented listing of files, which is colorized ala dircolors if the LS_COLORS environment variable is set and output is to tty.
trimgalorebioTrim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.
trimmomaticbioTrimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.
trinityTrinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.
ucsc-toolsbioA set of genome utilities developed at the University of California Santa Cruz.
udunitstoolsUDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.
unrartoolsRAR is a powerful archive manager.
vaporvisVAPOR is the Visualization and Analysis Platform for Ocean, Atmosphere, and Solar Researchers. VAPOR provides an interactive 3D visualization environment that can also produce animations and still frame images
varscanbioVarScan - Variant calling and somatic mutation/CNV detection for next-generation sequencing data
vaspchemThe Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling.
vcellbioVCell (Virtual Cell) is a comprehensive platform for modeling cell biological systems that is built on a central database and disseminated as a web application.
vcftoolsbioThe aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
velvetbioSequence assembler for very short reads
vgbioVariation graphs provide a succinct encoding of the sequences of many genomes.
viennarnabioThe Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
vigravisVIGRA stands for "Vision with Generic Algorithms". It's an image processing and analysis library that puts its main emphasis on customizable algorithms and data structures. VIGRA is especially strong for multi-dimensional images, because many algorithms (e.g. filters, feature computation, superpixels) are implemented for arbitrary high dimensions.
visitvisVisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.
vmdchemVMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
voro++mathVoro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles.
vsearchbioVSEARCH which supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.
vtkvisThe Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.
wannier90chemWannier90 is a package to calculate maximally-localised Wannier functions.
waspbioWASP is a suite of tools for unbiased allele-specific read mapping and discovery of molecular QTLs.
wdltooltoolsA Java command-line tool co-developed with WDL that performs utility functions, including syntax validation and generation of input JSON templates.
wigtobigwigbioThe bigWig format is useful for dense, continuous data that will be displayed in the Genome Browser as a graph. BigWig files are created from wiggle (wig) type files using the program wigToBigWig.
wxpythonviswxPython is a GUI toolkit for the Python programming language. It allows Python programmers to create programs with a robust, highly functional graphical user interface, simply and easily. It is implemented as a Python extension module (native code) that wraps the popular wxWidgets cross platform GUI library, which is written in C++.
wxwidgetsviswxPython is a GUI toolkit for the Python programming language. It allows Python programmers to create programs with a robust, highly functional graphical user interface, simply and easily. It is implemented as a Python extension module (native code) that wraps the popular wxWidgets cross platform GUI library, which is written in C++.
xcrysdenvisXCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.
xercestoolsXerces-C++ is a validating XML parser written in a portable subset of C++.
xxdifftoolsxxdiff is a graphical file and directories comparator and merge tool.
yaffchemYaff stands for 'Yet another force field'. It is a pythonic force-field code.
yamboYAMBO implements Many-Body Perturbation Theory (MBPT) methods (such as GW and BSE) and Time-Dependent Density Functional Theory (TDDFT), which allows for accurate prediction of fundamental properties as band gaps of semiconductors, band alignments, defect quasi-particle energies, optics and out-of-equilibrium properties of materials.
yasmlangYasm: Complete rewrite of the NASM assembler with BSD license
zstdlibZstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set.