List of open source bioinformatics software
Encyclopedia
This is a list of open source
Open source
The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...

 bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...

 software
with articles in Wikipedia.
Software Description Resources Platform License Developer
Anduril
Anduril (workflow engine)
Anduril is an open source component-based workflow framework for scientific data analysis developed at the Computational Systems Biology Laboratory, University of Helsinki....

Component-based workflow
Workflow
A workflow consists of a sequence of connected steps. It is a depiction of a sequence of operations, declared as work of a person, a group of persons, an organization of staff, or one or more simple or complex mechanisms. Workflow may be seen as any abstraction of real work...

 framework for data analysis
Website Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

, Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

, Windows
GPL University of Helsinki
University of Helsinki
The University of Helsinki is a university located in Helsinki, Finland since 1829, but was founded in the city of Turku in 1640 as The Royal Academy of Turku, at that time part of the Swedish Empire. It is the oldest and largest university in Finland with the widest range of disciplines available...

AutoDock
Protein-ligand docking
Protein–ligand docking is a molecular modelling technique. The goal of protein-ligand docking is to predict the position and orientation of a ligand when it is bound to a protein receptor or enzyme...

suite of automated docking tools Website Platform License Developer
Biochemical Algorithms Library (BALL)
BALL
The open source project BALL consists of the versatile C++ class framework BALL , a library of algorithms and data structures targeting molecular modelling and computational structural bioinformatics, a Python interface to this library and the open source graphical interface to BALL, the molecular...

C++ library and framework for molecular modeling and visualization designed for rapid prototyping Website - Articles Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

, Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

, Windows
LGPL BALL project team
Bioclipse
Bioclipse
The Bioclipse project is a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform...

Visual platform for chemo
Cheminformatics
Cheminformatics is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery...

- and bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...

 based on the Eclipse
Eclipse (software)
Eclipse is a multi-language software development environment comprising an integrated development environment and an extensible plug-in system...

 Rich Client Platform (RCP).
Website Platform Eclipse Public License
Eclipse Public License
The Eclipse Public License is an open source software license used by the Eclipse Foundation for its software. It replaces the Common Public License and removes certain terms relating to litigations related to patents....

The Bioclipse Project
Bioconductor
Bioconductor
Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology....

R (programming language)
R (programming language)
R is a programming language and software environment for statistical computing and graphics. The R language is widely used among statisticians for developing statistical software, and R is widely used for statistical software development and data analysis....

 language toolkit
Website - Articles Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

, Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

, Windows
Artistic License 2.0
Artistic License
The Artistic License refers most commonly to the original Artistic License , a software license used for certain free and open source software packages, most notably the standard Perl implementation and most CPAN modules, which are dual-licensed under the Artistic License and the GNU General Public...

Fred Hutchinson Cancer Research Center
Fred Hutchinson Cancer Research Center
The Fred Hutchinson Cancer Research Center, is one of the world’s leading cancer research institutes...

Bioinformatics Learning Tutorial (BLT) Educational interactive tutorials and 3D animations for Replication, Transcription, and Translation Project Home - Download for Windows Windows (stand-alone
Stand-alone
Standalone software can mean:* Computer software that can work offline, i.e. does not necessarily require network connection to function* Software that is not a part of some software bundle...

), Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

 & Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

 (source code
Source code
In computer science, source code is text written using the format and syntax of the programming language that it is being written in. Such a language is specially designed to facilitate the work of computer programmers, who specify the actions to be performed by a computer mostly by writing source...

 only with Qt
QT
- Units and measurements :* Quart, a measure of volume in traditional systems of units* Quarter, a unit of mass in Imperial units, equal to 2 stones or a quarter of a long hundredweight; one quarter = 12.70058636 kg* QT interval, a measurement used in cardiology...

 libraries)
Academic Free License
Academic Free License
The Academic Free License is a permissive free software license written in 2002 by Lawrence E. Rosen, the general counsel of the Open Source Initiative ....

Collaborative project
BioHaskell Haskell (programming language)
Haskell (programming language)
Haskell is a standardized, general-purpose purely functional programming language, with non-strict semantics and strong static typing. It is named after logician Haskell Curry. In Haskell, "a function is a first-class citizen" of the programming language. As a functional programming language, the...

Project web site -
Bioinformatics software in Haskell]
Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

, Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

, Windows
GPL, LGPL, and BSD Collaborative project
BioJava
BioJava
The BioJava Project is an open source project dedicated to providing Java tools for processing biological data. This includes include objects for manipulating sequences, protein structures, file parsers, CORBA interoperability, DAS, access to AceDB, dynamic programming, and simple statistical...

Java (programming language)
Java (programming language)
Java is a programming language originally developed by James Gosling at Sun Microsystems and released in 1995 as a core component of Sun Microsystems' Java platform. The language derives much of its syntax from C and C++ but has a simpler object model and fewer low-level facilities...

Website Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

, Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

, Windows
LGPL v2.1 Open Bioinformatics Foundation
Open Bioinformatics Foundation
The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics....

BioMOBY
BioMOBY
BioMOBY is a registry of web services used in bioinformatics. It allows interoperability between biological data hosts and analytical services by annotating services with terms taken from standard ontologies.- The BioMOBY project :...

registry of web services Website - Articles Web License Open Bioinformatics Foundation
Open Bioinformatics Foundation
The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics....

BioPerl
BioPerl
BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the Human Genome Project....

Perl
Perl
Perl is a high-level, general-purpose, interpreted, dynamic programming language. Perl was originally developed by Larry Wall in 1987 as a general-purpose Unix scripting language to make report processing easier. Since then, it has undergone many changes and revisions and become widely popular...

 language toolkit
Website Cross-platform Artistic License
Artistic License
The Artistic License refers most commonly to the original Artistic License , a software license used for certain free and open source software packages, most notably the standard Perl implementation and most CPAN modules, which are dual-licensed under the Artistic License and the GNU General Public...

 & GPL
Open Bioinformatics Foundation
Open Bioinformatics Foundation
The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics....

BioPHP
BioPHP
BioPHP is a package of Open Source PHP code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other Bioinformatics tools.-External links:**...

PHP
PHP
PHP is a general-purpose server-side scripting language originally designed for web development to produce dynamic web pages. For this purpose, PHP code is embedded into the HTML source document and interpreted by a web server with a PHP processor module, which generates the web page document...

 language toolkit
Website Platform License Open Bioinformatics Foundation
Open Bioinformatics Foundation
The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics....

Biopython
BioPython
The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology, as well as bioinformatics.-References:*refer to the Biopython website for other , and a list of over one hundred ....

Python
Python (programming language)
Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive...

 language toolkit
Website Cross-platform Biopython License Open Bioinformatics Foundation
Open Bioinformatics Foundation
The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics....

BioRails
BioRails
BioRails is a data management system designed to support researchers in drug discovery. It facilitates the capture of structured end-point data that can be queried and data mined in a relational database...

a data management system designed to support researchers in drug discovery
Drug discovery
In the fields of medicine, biotechnology and pharmacology, drug discovery is the process by which drugs are discovered or designed.In the past most drugs have been discovered either by identifying the active ingredient from traditional remedies or by serendipitous discovery...

Website Platform License Developer
BioRuby
BioRuby
BioRuby is a package of Open Source Ruby code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other Bioinformatics tools. Recently, tools for structural biology have been added.-External links:* ,*...

Ruby
Ruby (programming language)
Ruby is a dynamic, reflective, general-purpose object-oriented programming language that combines syntax inspired by Perl with Smalltalk-like features. Ruby originated in Japan during the mid-1990s and was first developed and designed by Yukihiro "Matz" Matsumoto...

 language toolkit
Website Platform License Open Bioinformatics Foundation
Open Bioinformatics Foundation
The Open Bioinformatics Foundation is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics....

caCORE ontologic representation environment Website - Articles Platform License National Cancer Institute
National Cancer Institute
The National Cancer Institute is part of the National Institutes of Health , which is one of 11 agencies that are part of the U.S. Department of Health and Human Services. The NCI coordinates the U.S...

caArray ontologic representation environment http://caarray.nci.nih.gov/documentation - https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/CaArray Platform License National Cancer Institute
National Cancer Institute
The National Cancer Institute is part of the National Institutes of Health , which is one of 11 agencies that are part of the U.S. Department of Health and Human Services. The NCI coordinates the U.S...

EMBOSS
EMBOSS
EMBOSS is an acronym for European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community...

Suite of packages for sequencing, searching, etc. Website Platform General Public Licence (GPL) and Library GPL Collaborative project
Galaxy
Galaxy (computational biology)
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience...

Scientific workflow
Scientific workflow system
A Scientific Workflow Systems is a specialized form of a workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or a workflow, in a scientific application...

 and data integration
Data integration
Data integration involves combining data residing in different sources and providing users with a unified view of these data.This process becomes significant in a variety of situations, which include both commercial and scientific domains...

 system
Website Unix-like
Unix-like
A Unix-like operating system is one that behaves in a manner similar to a Unix system, while not necessarily conforming to or being certified to any version of the Single UNIX Specification....

License Penn State and Emory University
Emory University
Emory University is a private research university in metropolitan Atlanta, located in the Druid Hills section of unincorporated DeKalb County, Georgia, United States. The university was founded as Emory College in 1836 in Oxford, Georgia by a small group of Methodists and was named in honor of...

GMOD
Generic Model Organism Database
The Generic Model Organism Database Project began as an effort to create reusable software tools for developing Model Organism Databases . MODs describe genome and other information about important experimental organisms in the life sciences...

Toolkit for addressing many common challenges at biological databases. Website Unix-like
Unix-like
A Unix-like operating system is one that behaves in a manner similar to a Unix system, while not necessarily conforming to or being certified to any version of the Single UNIX Specification....

 (server), Web browser
Web browser
A web browser is a software application for retrieving, presenting, and traversing information resources on the World Wide Web. An information resource is identified by a Uniform Resource Identifier and may be a web page, image, video, or other piece of content...

 (client)
Varies depending on tool Collaborative project
GENtle
GENtle (software)
- Features :GENtle is an equivalent to the proprietary Vector NTI, a handy tool for molecular biologists to analyze and edit DNA sequence files. Invitrogens removal of the free-of-cost academic licence for Vector NTI v11 has had a severe impact on many molecular biology labs that have come to rely...

An equivalent to the proprietary Vector NTI
Vector NTI
Vector NTI is a bioinformatics software package. The current versions are v11.5.1 for Windows/PCs and v7.1 for Macs, but only supporting Mac OS X v10.3 .- Features :* create, annotate, analyse, and share DNA/protein sequences...

, a tool to analyze and edit DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

 sequence files
Website Platform GPL Magnus Manske
Integrated Genome Browser
Integrated Genome Browser
Integrated Genome Browser is an open source genome browser, a visualization tool used to observe biologically-interesting patterns in genomic data sets, including sequence data, gene models, alignments, and data from DNA microarrays.- History :...

Java-based desktop genome browser
Genome browser
A genome browser is a graphical interface for display of information from a biological database for genomic data. Genome browsers enable researchers to visualize and browse entire genomes with annotated data including gene prediction and structure, proteins, expression, regulation, variation,...

Website Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

, Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

, Windows
CPL 1.0
Common Public License
In computing, the CPL is a free software / open-source software license published by IBM. The Free Software Foundation and Open Source Initiative have approved the license terms of the CPL....

GenoViz
IntAct
Intact
Intact can refer to:*Intact , a Romanian media trust*Intact and "Intact" by Ned's Atomic Dustbin*Intacto, a film*Entire , describing an animal that has not been spayed or neutered*Genital integrity...

molecular interaction database Website - Articles Platform License European Bioinformatics Institute
European Bioinformatics Institute
The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...

Java Treeview microarray data viewer Website - Articles Cross-platform License Developer
LabKey Server
LabKey Server
LabKey Server is free, open source software available for scientists to integrate, analyze, and share biomedical research data. The platform provides a secure data repository that allows web-based querying, reporting, and collaborating across a range of data sources...

platform for integrating, analyzing and sharing data Website Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

, Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

, Windows
Apache License
Apache License
The Apache License is a copyfree free software license authored by the Apache Software Foundation . The Apache License requires preservation of the copyright notice and disclaimer....

LabKey Software Foundation
OpenClinica software for capturing and managing data in clinical trials Website Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

, Windows
LGPL OpenClinica
REDCRAFT software for determining tertiary protein structure given assigned Residual Dipolar Coupling data Website Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

, Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

, Windows
GPL v3 REDCRAFT
SAM Tools Data format (SAM) and accompanying tool suite, for storing large nucleotide sequence alignments Website Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

BSD, MIT License
MIT License
The MIT License is a free software license originating at the Massachusetts Institute of Technology . It is a permissive license, meaning that it permits reuse within proprietary software provided all copies of the licensed software include a copy of the MIT License terms...

1000 Genomes Project
Taverna workbench
Taverna workbench
Taverna Workbench is an open source software tool for designing and executing workflows, created by the myGrid project and funded through the OMII-UK...

Tool for designing and executing workflows Website Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

, Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

, Windows
LGPL myGrid
MyGrid
The myGrid consortium is a multi-institutional, multi-disciplinary internationally leading research group focussing on the challenges of eScience...

UGENE
UGENE
UGENE is free open-source cross-platform bioinformatics software.It integrates dozens of well-known biological tools and algorithms, providing both graphical user and command line interfaces...

integrated bioinformatics tools Website - Podcast Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...

, Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...

, Windows
GPL2 License Unipro

See also


External links

  • Bio-Informatics software - SourceForge
    SourceForge
    SourceForge Enterprise Edition is a collaborative revision control and software development management system. It provides a front-end to a range of software development lifecycle services and integrates with a number of free software / open source software applications .While originally itself...

  • Free Biology Software - Free Software Directory
    Free Software Directory
    The Free Software Directory is a project of the Free Software Foundation . It catalogs free software that runs under free operating systems - particularly GNU and Linux. The project was formerly co-run by UNESCO....

     - Free Software Foundation
    Free Software Foundation
    The Free Software Foundation is a non-profit corporation founded by Richard Stallman on 4 October 1985 to support the free software movement, a copyleft-based movement which aims to promote the universal freedom to create, distribute and modify computer software...

  • Bioinformatics Links Directory
The source of this article is wikipedia, the free encyclopedia.  The text of this article is licensed under the GFDL.
 
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