List of open-source bioinformatics software
This is a list of open-source bioinformatics software with articles in Wikipedia.
| Software | Description | Platform | License | Developer |
|---|---|---|---|---|
| .NET Bio | A language-neutral bioinformatics toolkit built using the Microsoft 4.0 .NET Framework to help developers, researchers, and scientists. | .NET Framework | Apache License | Collaborative project |
| AMPHORA | Metagenomics analysis software | Linux | GNU General Public License | Developer |
| Anduril | Component-based workflow framework for data analysis | Linux, Mac OS X, Windows | GPL | University of Helsinki |
| AutoDock | suite of automated docking tools | Platform | GNU GPL | Developer |
| Biochemical Algorithms Library (BALL) | C++ library and framework for molecular modeling and visualization designed for rapid prototyping | Linux, Mac OS X, Windows | LGPL | BALL project team |
| Bioclipse | Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). | Platform | Eclipse Public License | The Bioclipse Project |
| Bioconductor | R (programming language) language toolkit | Linux, Mac OS X, Windows | Artistic License 2.0 | Fred Hutchinson Cancer Research Center |
| BioJava | Java (programming language) | Linux, Mac OS X, Windows | LGPL v2.1 | Open Bioinformatics Foundation |
| BioJS | Javascript | Web | Apache License | - |
| BioMOBY | registry of web services | Web | Artistic License | Open Bioinformatics Foundation |
| BioPerl | Perl language toolkit | Cross-platform | Artistic License & GPL | Open Bioinformatics Foundation |
| BioPHP | PHP language toolkit | Platform | GPL v2 | Open Bioinformatics Foundation |
| Biopython | Python language toolkit | Cross-platform | Biopython License | Open Bioinformatics Foundation |
| BioRuby | Ruby language toolkit | Platform | GNU GPL v2 or Ruby license | Open Bioinformatics Foundation |
| EMBOSS | Suite of packages for sequencing, searching, etc. | Platform | General Public Licence (GPL) and Library GPL | Collaborative project |
| FACS | FACS machine output analyzer. Percentage to absolute cell numbers. | Linux, Mac OS X, Windows | MIT | LogIN- |
| Galaxy | Scientific workflow and data integration system | Unix-like | Academic Free License | Penn State and Emory University |
| GenePattern | Scientific workflow system that provides access to more than 150 genomic analysis tools | Unix-like (public server); Linux, Mac OS X, Windows | MIT license | Broad Institute |
| GeWorkbench | Genomic data integration platform | Linux, Mac OS X, Windows | License | Columbia University |
| GMOD | Toolkit for addressing many common challenges at biological databases. | Unix-like (server), Web browser (client) | Varies depending on tool | Collaborative project |
| GenGIS | Application that allows users to combine digital map data with information about biological sequences collected from the environment. | Windows, Mac OS X | GPL | Collaborative project |
| GenomeSpace | Centralized web application that provides data format transformations and facilitates connections with other bioinformatics tools | Web browser | LGPL | Broad Institute, Collaborative project |
| GENtle | An equivalent to the proprietary Vector NTI, a tool to analyze and edit DNA sequence files | Platform | GPL | Magnus Manske |
| Integrated Genome Browser | Java-based desktop genome browser | Linux, Mac OS X, Windows | CPL 1.0 | GenoViz |
| InterMine | Extensive data warehouse system for the analysis and integration of biological datasets | Cross-platform | LGPL | University of Cambridge |
| LabKey Server | platform for integrating, analyzing and sharing data | Linux, Mac OS X, Windows | Apache License | LabKey Software Foundation |
| LeoTask | A lightweight & reliable framework for running computational tasks in parallel and aggregating the results (MapReduce) on a multicore computer | Linux, Mac OS X, Windows | FreeBSD License | University College London |
| PathVisio | a desktop software for drawing, analysis and visualization of biological pathways | Linux, Mac OS X, Windows | Apache 2.0 License | Maastricht University |
| Orange | a component-based data mining and machine learning software suite, featuring a visual programming front-end for explorative data analysis and visualization, and Python bindings and libraries for scripting | Linux, Mac OS X, Windows | GPL | University of Ljubljana |
| Staden Package | Sequence assembly, editing and analysis, primarily consisting of gap4, gap5 and spin. | Linux, Mac OS X, Windows | BSD | Wellcome Trust Sanger Institute / Medical Research Council |
| STAMP | Software package for analyzing metagenomic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. | Windows, Mac OS X | GPL | Collaborative project |
| Taverna workbench | Tool for designing and executing workflows | Linux, Mac OS X, Windows | LGPL | myGrid |
| UGENE | integrated bioinformatics tools | Linux, Mac OS X, Windows | GPL2 | Unipro |
See also
- List of sequence alignment software
- List of open-source healthcare software
- List of biomedical cybernetics software
- List of freeware health software
- List of molecular graphics systems
- List of software for molecular mechanics modeling