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List of open-source bioinformatics software

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Title: List of open-source bioinformatics software  
Author: World Heritage Encyclopedia
Language: English
Subject: Bioinformatics
Collection: Bioinformatics Software, Free Bioinformatics Software, Free Software Lists and Comparisons
Publisher: World Heritage Encyclopedia

List of open-source bioinformatics software

This is a list of open-source bioinformatics software with articles in WorldHeritage.

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
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
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
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

External links

  • Free Biology Software – Free Software DirectoryFree 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

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