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List of open-source bioinformatics software

From Wikipedia, the free encyclopedia

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 Jonathan Eisen
Anduril Component-based workflow framework for data analysis Linux, macOS, Windows GPL University of Helsinki
Apache Taverna Written in Java Linux, macOS, Windows Apache License 2.0 Apache Software Foundation, myGrid
Ascalaph Designer Computer program for general purpose molecular modelling for molecular design and simulations. Windows GPLv2 Agile Molecule
AutoDock Suite of automated docking tools Linux, Mac OS X, SGI IRIX, and Windows GPL Scripps Research
Avogadro C++ (Qt) based molecule editor and visualizer for in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Linux, macOS, Unix, Windows 3-Clause BSD License Open Chemistry Project
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) Linux, macOS, Windows[1] 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 BioJS Community
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[2] Open Bioinformatics Foundation
BioRuby Ruby language toolkit Linux, macOS, Windows[3] 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. Linux, macOS, Windows GPL and LGPL Free open source GNU GPLv2 or later
EMBOSS Suite of packages for sequencing, searching, etc. written in C Linux, macOS, Unix, Windows[4] 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[5] 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
GenoCAD A computer-assisted design (CAD) tool for synthetic biology, used to design genetic constructs based on grammar rules. Linux, macOS, Windows Apache License 2.0 GenoCAD Team (Virginia Bioinformatics Institute)
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 Linux, macOS, Windows GPL Magnus Manske
gget Efficient querying of genomic reference databases including UniProt, National Center for Biotechnology Information, and Ensembl genome database project Linux, macOS, Windows BSD Laura Luebbert and Lior Pachter
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
Nextflow A workflow management system used for building and running scalable and reproducible bioinformatics pipelines, especially in cloud and high-performance computing environments. Linux, macOS, Windows Apache License 2.0 Nextflow Team[6]
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 GNU (GPL) v3 Université du Québec à Montréal[7]
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

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References

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  1. ^ https://www.researchgate.net/publication/6490579_Bioclipse_An_open_source_workbench_for_chemo-_and_bioinformatics
  2. ^ Biopython License
  3. ^ https://academic.oup.com/bioinformatics/article/26/20/2617/194139#
  4. ^ https://emboss.sourceforge.net/download/
  5. ^ "GeWorkbench License". geWorkbench. Columbia University. 15 June 2014.
  6. ^ https://www.genengnews.com/sponsored/empowering-scientific-research-with-nextflow-ai/
  7. ^ http://www.trex.uqam.ca/
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