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List of open-source bioinformatics software

From Wikipedia, the free encyclopedia

This is a list of computer software which is made for bioinformatics and released under open-source software licenses with articles in Wikipedia.

Software Description Platform License Developer
.NET Bio Language-neutral toolkit built using the Microsoft 4.0 .NET Framework to help developers, researchers, and scientists .NET FrameworkApacheCollaborative project
AMPHORAMetagenomics analysis software LinuxGPLJonathan Eisen
AndurilComponent-based workflow framework for data analysis Linux, macOS, WindowsGPLUniversity of Helsinki
Apache TavernaWritten in JavaLinux, macOS, WindowsApache License 2.0 Apache Software Foundation, myGrid
Ascalaph DesignerComputer program for general purpose molecular modelling for molecular design and simulations. WindowsGPLv2Agile Molecule
AutoDockSuite of automated docking tools Linux, Mac OS X, SGI IRIX, and WindowsGPLScripps Research
AvogadroC++ (Qt) based molecule editor and visualizer for in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Linux, macOS, Unix, Windows3-Clause BSD LicenseOpen Chemistry Project
BEDtools"Genome arithmetic"—manipulation of coordinate sets and the extraction of sequences from a BED file. LinuxMITQuinlanLab, University of Utah
BioclipseVisual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP) Linux, macOS, Windows[1]Eclipse PublicThe Bioclipse Project
BioconductorR (programming language) language toolkit Linux, macOS, WindowsArtistic 2.0 Fred Hutchinson Cancer Research Center
BioJavaJava library functions for manipulating sequences, protein structures, file parsers, CORBA interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines Linux, macOS, WindowsLGPL v2.1 Open Bioinformatics Foundation
BioJSJavaScript library of components to visualize biological data Web browserApacheBioJS Community
BioMOBYRegistry of web servicesWeb browserArtisticOpen Bioinformatics Foundation
BioPerlPerl language toolkit Cross-platformArtistic, GPLOpen Bioinformatics Foundation
BioPHPPHP language toolkit with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools Cross-platformGPL v2 Open Bioinformatics Foundation
BiopythonPython language toolkit Cross-platformBiopython[2]Open Bioinformatics Foundation
BioRubyRuby language toolkit Linux, macOS, Windows[3]GPL v2 or RubyOpen Bioinformatics Foundation
BLASTAlgorithm and program for comparing primary biological sequence information, including DNA and protein sequences. Cross-platformPublic domainNational Center for Biotechnology Information
CP2KPerform atomistic simulations of solid state, liquid, molecular and biological systems, written in Fortran 2003. Linux, macOS, WindowsGPL and LGPLFree open source GNU GPLv2 or later
EMBOSSSuite of packages for sequencing, searching, etc. written in CLinux, macOS, Unix, Windows[4]GPL and LGPLCollaborative project
GalaxyScientific workflow and data integration system Unix-likeAcademic FreeCollaborative project
GenePatternScientific workflow system that provides access to hundreds of genomic analysis tools Unix-like (public server); Linux, macOS, WindowsMITBroad Institute, UC San Diego
GeworkbenchGenomic data integration platform Linux, macOS, WindowsGeWorkbench License[5]Columbia University
GMODToolkit to address many common challenges at biological databases Unix-like (server), Web browser (client) Varies depending on tool Collaborative project
GenGISApplication that allows combining digital map data with information about biological sequences collected from the environment Windows, macOSGPLCollaborative project
GenoCADA computer-assisted design (CAD) tool for synthetic biology, used to design genetic constructs based on grammar rules. Linux, macOS, WindowsApache License 2.0 GenoCAD Team (Virginia Bioinformatics Institute)
GenomespaceCentralized web application that provides data format transformations and facilitates connections with other bioinformatics tools Web browserLGPLBroad Institute, collaborative project
GENtleAn equivalent to the proprietary Vector NTI, a tool to analyze and edit DNA sequence files Linux, macOS, WindowsGPLMagnus Manske
ggetEfficient querying of genomic reference databases including UniProt, National Center for Biotechnology Information, and Ensembl genome database projectLinux, macOS, WindowsBSDLaura Luebbert and Lior Pachter
GROMACSMolecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. Linux, macOS, WindowsCommon Public 1.0 GenoViz
Integrated Genome BrowserJava-based desktop genome browserLinux, macOS, WindowsCommon Public 1.0 GenoViz
InterMineExtensive data warehouse system for the analysis and integration of biological datasets written in Java and JavaScript Cross-platformLGPLUniversity of Cambridge
LabKey ServerSoftware platform, allows organizations to integrate, analyze, and share complex biomedical data Linux, macOS, WindowsApacheLabKey Software Foundation
LAMMPSMolecular dynamics program written in C++Linux, macOS, WindowsApacheSandia National Laboratories.
mothurSoftware for analysis of 16S rRNA gene amplicon sequence data Linux, macOS, WindowsGPLUniversity of Michigan
NextflowA workflow management system used for building and running scalable and reproducible bioinformatics pipelines, especially in cloud and high-performance computing environments. Linux, macOS, WindowsApache License 2.0 Nextflow Team[6]
PathVisioDesktop software for drawing, analyzing, and visualizing biological pathways Linux, macOS, WindowsApache 2.0 Maastricht University
OrangeComponent-based data mining and machine learning software suite written in C++, featuring a visual programming front-end for exploratory data analysis and interactive visualization, and Python bindings and libraries for scripting Linux, macOS, WindowsGPLUniversity of Ljubljana
SAMtoolsUtilities for interacting with high-throughput sequencing data and alignments in sam/bam format Unix/LinuxMITCollaborative project
SOAP SuiteSuite of tools for assembly, alignment, and analysis of short read next generation sequencing data Unix/Linux, macOSGPLBGI
Staden PackageSequence assembly, editing, and analysis, mainly consisting of gap4, gap5, and spin. Written in C, C++, Fortran and Tcl. Linux, macOS, WindowsBSDWellcome Trust Sanger Institute, Medical Research Council
Taverna workbenchTool to design and execute workflows Linux, macOS, WindowsLGPLmyGrid
T-REX (web server)Inference, validation and visualization of phylogenetic trees and phylogenetic networks Web browser, WindowsGNU (GPL) v3 Université du Québec à Montréal[7]
UGENEIntegrated bioinformatics tools, written in C++ (Qt) Linux, macOS, WindowsGPL 2 Unipro
UnipeptMetaproteomics biodiversity analysis written in Ruby and JavaScript Web browserMITGhent University
VOTCAA Coarse-grained modeling package for molecular dynamics, written in C++, Perl, BASH Linux, macOS, Windows, any other Unix variety Apache License 2.0Max Planck Institute for Polymer Research

See also

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References

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  1. ^https://www.researchgate.net/publication/6490579_Bioclipse_An_open_source_workbench_for_chemo-_and_bioinformatics
  2. ^Biopython License
  3. ^Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki (2010). "BioRuby: Bioinformatics software for the Ruby programming language". Bioinformatics. 26 (20): 2617–2619. doi:10.1093/bioinformatics/btq475. PMID 20739307.
  4. ^"EMBOSS Downloads".
  5. ^"GeWorkbench License". geWorkbench. Columbia University. 15 June 2014.
  6. ^"Empowering Scientific Research with Nextflow + AI". 3 December 2024.
  7. ^http://www.trex.uqam.ca/
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