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 |
| BuddySuite | Command-line toolkits for working with sequence, alignment, and phylogenetic tree files | Linux, Mac OS X | Public Domain | National Human Genome Research Institute |
| 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 | Open-source software platform that allows organizations to integrate, analyze and share complex biomedical data | Linux, Mac OS X, Windows | Apache License | LabKey Software Foundation |
| LARVA | LARVA is a computational framework designed to facilitate the study of noncoding variants in cancer genomes, using a statistical model that accounts for the highly heterogeneous mutation rate of noncoding elements throughout the genome to identify statistically significant mutation enrichments. | Linux, Mac OS X, Docker | Yale University | |
| mothur | Software for analysis of the 16S rRNA gene | Linux, Mac OS X, Windows | The University of Michigan | |
| PathVisio | a desktop software for drawing, analysis and visualization of biological pathways | Linux, Mac OS X, Windows | Apache 2.0 License | Maastricht University |
| PromKappa | DNA pattern analysis and visualization. | Windows | GPL | University of Bucharest |
| ProSSA | (Hydrogen-Bond-Independent) Proteins' Secondary Structure Assignment | Web | Bioinformatics Center | |
| PyPDB | Python querying API for the Protein Data Bank | Linux, Mac OS X, Windows | MIT License | Stanford University |
| RaFoSA | Random Forests Secondary Structure Assignment When All-Atom Information is Lacking | Linux, Mac OS X, Windows | Bioinformatics Center | |
| Orange | a component-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 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 |
| TRAL | Python language toolkit for the annotation and analysis of sequence tandem repeats. | Linux, Mac OS X, Windows | GPL | Collaborative project |
| UGENE | integrated bioinformatics tools | Linux, Mac OS X, Windows | GPL2 | Unipro |
| Unipept | Metaproteomics biodiversity analysis | Web browser | MIT License | Ghent University |
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
External links
- Free Biology Software – Free Software Directory – Free Software Foundation
- Bioinformatics Links Directory
- Click2Drug and VLS3D are Websites that list in silico tools and databases (in general free to all users)
- LabWorm - comprehensive portal for free online bioinformatics resources
developed by the scientific community in the area of drug design, structural bioinformatics and drug discovery