List_of_open-source_bioinformatics_software

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.

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Biopython License

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"GeWorkbench License". geWorkbench. Columbia University. 15 June 2014.

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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	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

List_of_open-source_bioinformatics_software

List of open-source bioinformatics software

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