List of open-source bioinformatics software

Short description: None

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

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.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 | C++ (Qt) based molecule editor and visualizer for in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.  | ?  | GPL | ?
BEDtools | "Genome arithmetic" -- manipulation of coordinate sets and the extraction of sequences from a BED file.  | Linux | MIT | QuinlanLab, University of Utah
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 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, Windows | LGPL v2.1  | Open Bioinformatics Foundation
BioJS | JavaScript library of components to visualize biological data  | 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 with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools  | Cross-platform  | 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
BLAST | Algorithm and program for comparing primary biological sequence information, including DNA and protein sequences.  | Cross-platform  | Public domain | National Center for Biotechnology Information
CP2K | Perform atomistic simulations of solid state, liquid, molecular and biological systems, written in Fortran 2003.  | ?  | GPL and LGPL | Free open source GNU GPLv2 or later
EMBOSS | Suite of packages for sequencing, searching, etc. written in C | ?  | 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 written in Java and JavaScript  | 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 written in C++ | Linux, macOS, Windows | Apache | Sandia National Laboratories.
mothur | Software for analysis of 16S rRNA gene amplicon sequence data  | Linux, macOS, Windows | GPL | University of Michigan
PathVisio | Desktop software for drawing, analyzing, and visualizing biological pathways  | Linux, macOS, Windows | Apache 2.0  | Maastricht University
Orange | Component-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, Windows | GPL | University of Ljubljana
SAMtools | Utilities for interacting with high-throughput sequencing data and alignments in sam/bam format  | Unix/Linux | MIT | Collaborative project
SOAP Suite | Suite of tools for assembly, alignment, and analysis of short read next generation sequencing data  | Unix/Linux, macOS | GPL | BGI
Staden Package | Sequence assembly, editing, and analysis, mainly consisting of gap4, gap5, and spin. Written in C, C++, Fortran and Tcl.  | Linux, macOS, Windows | BSD | Wellcome Trust Sanger Institute, Medical Research Council
Taverna workbench  | Tool to design and execute workflows  | Linux, macOS, Windows | LGPL | myGrid
T-REX (web server) | Inference, validation and visualization of phylogenetic trees and phylogenetic networks  | Web browser, Windows | ?  | Université du Québec à Montréal
UGENE | Integrated bioinformatics tools, written in C++ (Qt)  | Linux, macOS, Windows | GPL 2  | Unipro
Unipept | Metaproteomics biodiversity analysis written in Ruby and JavaScript  | Web browser | MIT | Ghent University
VOTCA | A Coarse-grained modeling package for molecular dynamics, written in C++, Perl, BASH  | 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
* List of systems biology modelling software
* Comparison of software for molecular mechanics modeling
* List of proprietary bioinformatics software

## References

1. ↑ Biopython License
2. ↑ "GeWorkbench License". Columbia University. 15 June 2014. http://wiki.c2b2.columbia.edu/workbench/index.php/GeWorkbench_License.

## External links

* Free Biology Software – Free Software Directory – Free Software Foundation

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