List of open-source bioinformatics software
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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 Framework | Apache | Collaborative project |
| AMPHORA | Metagenomics analysis software | Linux | GPL | ? |
| Anduril | Component-based workflow framework for data analysis | Linux, macOS, Windows | GPL | University of Helsinki |
| Ascalaph Designer | Computer program for general purpose molecular modelling for molecular design and simulations. | ? | GPLv2 | Agile Molecule |
| AutoDock | Suite of automated docking tools | ? | GPL | ? |
| Avogadro | Molecule editor and visualizer for in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | ? | GPL | ? |
| Bioclipse | Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP) | ? | Eclipse Public | The Bioclipse Project |
| Bioconductor | R (programming language) language toolkit | Linux, macOS, Windows | Artistic 2.0 | Fred Hutchinson Cancer Research Center |
| BioJava | Java | Linux, macOS, Windows | LGPL v2.1 | Open Bioinformatics Foundation |
| BioJS | JavaScript | Web browser | Apache | ? |
| BioMOBY | Registry of web services | Web browser | Artistic | Open Bioinformatics Foundation |
| BioPerl | Perl language toolkit | Cross-platform | Artistic, GPL | Open Bioinformatics Foundation |
| BioPHP | PHP language toolkit | ? | GPL v2 | Open Bioinformatics Foundation |
| Biopython | Python language toolkit | Cross-platform | Biopython[1] | Open Bioinformatics Foundation |
| BioRuby | Ruby language toolkit | ? | GPL v2 or Ruby | Open Bioinformatics Foundation |
| CP2K | Perform atomistic simulations of solid state, liquid, molecular and biological systems. | ? | GPL and LGPL | Free open source GNU GPLv2 or later |
| EMBOSS | Suite of packages for sequencing, searching, etc. | ? | GPL and LGPL | Collaborative project |
| Galaxy | Scientific workflow and data integration system | Unix-like | Academic Free | Collaborative project |
| GenePattern | Scientific workflow system that provides access to hundreds of genomic analysis tools | Unix-like (public server); Linux, macOS, Windows | MIT | Broad Institute, UC San Diego |
| Geworkbench | Genomic data integration platform | Linux, macOS, Windows | GeWorkbench License[2] | Columbia University |
| GMOD | Toolkit to address many common challenges at biological databases | Unix-like (server), Web browser (client) | Varies depending on tool | Collaborative project |
| GenGIS | Application that allows combining digital map data with information about biological sequences collected from the environment | Windows, macOS | 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 | ? | GPL | Magnus Manske |
| GROMACS | Molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. | Linux, macOS, Windows | Common Public 1.0 | GenoViz |
| Integrated Genome Browser | Java-based desktop genome browser | Linux, macOS, Windows | Common Public 1.0 | GenoViz |
| InterMine | Extensive data warehouse system for the analysis and integration of biological datasets | Cross-platform | LGPL | University of Cambridge |
| LabKey Server | Software platform, allows organizations to integrate, analyze, and share complex biomedical data | Linux, macOS, Windows | Apache | LabKey Software Foundation |
| LAMMPS | Molecular dynamics program | Linux, macOS, Windows | Apache | Sandia National Laboratories. |
| mothur | Software for analysis of the 16S rRNA gene | Linux, macOS, Windows | ? | University of Michigan |
| PathVisio | Desktop software for drawing, analysing, and visualizing biological pathways | Linux, macOS, Windows | Apache 2.0 | Maastricht University |
| Orange | 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, macOS, Windows | GPL | University of Ljubljana |
| Staden Package | Sequence assembly, editing, and analysis, mainly consisting of gap4, gap5, and spin. | Linux, macOS, Windows | BSD | Wellcome Trust Sanger Institute, Medical Research Council |
| Taverna workbench | Tool to design and execute workflows | Linux, macOS, Windows | LGPL | myGrid |
| UGENE | Integrated bioinformatics tools | Linux, macOS, Windows | GPL 2 | Unipro |
| Unipept | Metaproteomics biodiversity analysis | Web browser | MIT | Ghent University |
| VOTCA | A Coarse-grained modeling package, | GNU/Linux, macOS, Windows, any other Unix variety | Apache License 2.0 | Max Planck Institute for Polymer Research |
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_genetic_engineering_software
- List of molecular graphics systems
- Comparison of software for molecular mechanics modeling
- List of proprietary bioinformatics software
References
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