List of open-source bioinformatics software


This is a list of computer software which is made for bioinformatics and released under open-source software licenses with articles in Wikipedia.
SoftwareDescriptionPlatformLicenseDeveloper
.NET BioLanguage-neutral toolkit built using the Microsoft 4.0.NET Framework to help developers, researchers, and scientists.NET FrameworkApacheCollaborative project
AMPHORAMetagenomics analysis softwareLinuxGPL
AndurilComponent-based workflow framework for data analysisLinux, macOS, WindowsGPLUniversity of Helsinki
Ascalaph DesignerComputer program for general purpose molecular modelling for molecular design and simulations.GPLv2Agile Molecule
AutoDockSuite of automated docking toolsGPL
AvogadroMolecule editor and visualizer for in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.GPL
BioclipseVisual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform Eclipse PublicThe Bioclipse Project
BioconductorR language toolkitLinux, macOS, WindowsArtistic 2.0Fred Hutchinson Cancer Research Center
BioJavaJavaLinux, macOS, WindowsLGPL v2.1Open Bioinformatics Foundation
BioJSJavaScriptWeb browserApache
BioMOBYRegistry of web servicesWeb browserArtisticOpen Bioinformatics Foundation
BioPerlPerl language toolkitCross-platformArtistic, GPLOpen Bioinformatics Foundation
BioPHPPHP language toolkitGPL v2Open Bioinformatics Foundation
BiopythonPython language toolkitCross-platformBiopythonOpen Bioinformatics Foundation
BioRubyRuby language toolkitGPL v2 or RubyOpen Bioinformatics Foundation
CP2KPerform atomistic simulations of solid state, liquid, molecular and biological systems.GPL and LGPLFree open source GNU GPLv2 or later
EMBOSSSuite of packages for sequencing, searching, etc.GPL and LGPLCollaborative project
GalaxyScientific workflow and data integration systemUnix-likeAcademic FreeCollaborative project
GenePatternScientific workflow system that provides access to hundreds of genomic analysis toolsUnix-like ; Linux, macOS, WindowsMITBroad Institute, UC San Diego
GeworkbenchGenomic data integration platformLinux, macOS, WindowsGeWorkbench LicenseColumbia University
GMODToolkit to address many common challenges at biological databasesUnix-like, Web browser Varies depending on toolCollaborative project
GenGISApplication that allows combining digital map data with information about biological sequences collected from the environmentWindows, macOSGPLCollaborative project
GenomespaceCentralized web application that provides data format transformations and facilitates connections with other bioinformatics toolsWeb browserLGPLBroad Institute, collaborative project
GENtleAn equivalent to the proprietary Vector NTI, a tool to analyze and edit DNA sequence filesGPLMagnus Manske
GROMACSMolecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids.Linux, macOS, WindowsCommon Public 1.0GenoViz
Integrated Genome BrowserJava-based desktop genome browserLinux, macOS, WindowsCommon Public 1.0GenoViz
InterMineExtensive data warehouse system for the analysis and integration of biological datasetsCross-platformLGPLUniversity of Cambridge
LabKey ServerSoftware platform, allows organizations to integrate, analyze, and share complex biomedical dataLinux, macOS, WindowsApacheLabKey Software Foundation
LAMMPSMolecular dynamics programLinux, macOS, WindowsApacheSandia National Laboratories.
mothurSoftware for analysis of the 16S rRNA geneLinux, macOS, WindowsUniversity of Michigan
PathVisioDesktop software for drawing, analysing, and visualizing biological pathwaysLinux, macOS, WindowsApache 2.0Maastricht University
OrangeComponent-based data mining and machine learning software suite, featuring a visual programming front-end for exploratory data analysis and interactive visualization, and Python bindings and libraries for scriptingLinux, macOS, WindowsGPLUniversity of Ljubljana
Staden PackageSequence assembly, editing, and analysis, mainly consisting of gap4, gap5, and spin.Linux, macOS, WindowsBSDWellcome Trust Sanger Institute, Medical Research Council
Taverna workbenchTool to design and execute workflowsLinux, macOS, WindowsLGPLmyGrid
UGENEIntegrated bioinformatics toolsLinux, macOS, WindowsGPL 2Unipro
UnipeptMetaproteomics biodiversity analysisWeb browserMITGhent University
VOTCAA Coarse-grained modeling package,GNU/Linux, macOS, Windows, any other Unix varietyApache License 2.0Max Planck Institute for Polymer Research