List of open-source bioinformatics software

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

Language-neutral toolkit built using

the Microsoft 4.0 .NET Framework .NET Collaborative
.NET Bio Apache
to help developers, researchers, and Framework project
scientists

AMPHORA Metagenomics analysis software Linux GPL ?

Component-based workflow Linux, macOS, University of

Anduril GPL
framework for data analysis Windows Helsinki

Computer program for general

Ascalaph
purpose molecular modelling for ? GPLv2 Agile Molecule
Designer
molecular design and simulations.

AutoDock Suite of automated docking tools ? GPL ?

C++ (Qt) based molecule editor and

visualizer for in computational
Avogadro chemistry, molecular modeling, ? GPL ?
bioinformatics, materials science,
and related areas.

"Genome arithmetic" -- manipulation QuinlanLab (http://

BEDtools of coordinate sets and the extraction Linux MIT quinlanlab.org/),
of sequences from a BED file. University of Utah

Visual platform for chemo- and

The Bioclipse
Bioclipse bioinformatics based on the Eclipse ? Eclipse Public
Project
Rich Client Platform (RCP)
Fred Hutchinson
R (programming language) language Linux, macOS,
Bioconductor Artistic 2.0 Cancer Research
toolkit Windows
Center

Java library functions for

manipulating sequences, protein
structures, file parsers, CORBA Open
Linux, macOS,
BioJava interoperability, Distributed LGPL v2.1 Bioinformatics
Windows
Annotation System (DAS), access Foundation
to AceDB, dynamic programming,
and simple statistical routines

JavaScript library of components to

BioJS Web browser Apache ?
visualize biological data
Open
BioMOBY Registry of web services Web browser Artistic Bioinformatics
Foundation

Open
BioPerl Perl language toolkit Cross-platform Artistic, GPL Bioinformatics
Foundation

PHP language toolkit with classes

for DNA and protein sequence Open
BioPHP analysis, alignment, database Cross-platform GPL v2 Bioinformatics
parsing, and other bioinformatics Foundation
tools
Open
Biopython Python language toolkit Cross-platform Biopython[1] Bioinformatics
Foundation

Open
GPL v2 or
BioRuby Ruby language toolkit ? Bioinformatics
Ruby
Foundation
 Algorithm and program for comparing
National Center for
primary biological sequence
BLAST Cross-platform Public domain Biotechnology
information, including DNA and
Information
protein sequences.
Perform atomistic simulations of
Free open source
solid state, liquid, molecular and
CP2K ? GPL and LGPL GNU GPLv2 or
biological systems, written in Fortran
later
2003.

Suite of packages for sequencing, Collaborative

EMBOSS ? GPL and LGPL
searching, etc. written in C project

Scientific workflow and data Collaborative

Galaxy Unix-like Academic Free
integration system project
Unix-like
Scientific workflow system that
(public server); Broad Institute,
GenePattern provides access to hundreds of MIT
Linux, macOS, UC San Diego
genomic analysis tools
Windows

Linux, macOS, GeWorkbench Columbia

Geworkbench Genomic data integration platform
Windows License[2] University

Unix-like
Varies
Toolkit to address many common (server), Web Collaborative
GMOD depending on
challenges at biological databases browser project
tool
(client)

Application that allows combining

digital map data with information Windows, Collaborative
GenGIS GPL
about biological sequences collected macOS project
from the environment

Centralized web application that

Broad Institute,
provides data format transformations
Genomespace Web browser LGPL collaborative
and facilitates connections with
project
other bioinformatics tools
An equivalent to the proprietary
GENtle Vector NTI, a tool to analyze and ? GPL Magnus Manske
edit DNA sequence files

Molecular dynamics package mainly

Linux, macOS, Common
GROMACS designed for simulations of proteins, GenoViz
Windows Public 1.0
lipids and nucleic acids.
Integrated
Java-based desktop genome Linux, macOS, Common
Genome GenoViz
browser Windows Public 1.0
Browser

Extensive data warehouse system

for the analysis and integration of University of
InterMine Cross-platform LGPL
biological datasets written in Java Cambridge
and JavaScript

Software platform, allows

Linux, macOS, LabKey Software
LabKey Server organizations to integrate, analyze, Apache
Windows Foundation
and share complex biomedical data
Molecular dynamics program written Linux, macOS, Sandia National
LAMMPS Apache
in C++ Windows Laboratories.

Software for analysis of 16S rRNA Linux, macOS, University of

mothur GPL
gene amplicon sequence data Windows Michigan

Desktop software for drawing,

Linux, macOS, Maastricht
PathVisio analyzing, and visualizing biological Apache 2.0
Windows University
pathways
 Component-based data mining and
machine learning software suite
written in C++, featuring a visual
Linux, macOS, University of
Orange programming front-end for GPL
Windows Ljubljana
exploratory data analysis and
interactive visualization, and Python
bindings and libraries for scripting
Utilities for interacting with high-
Collaborative
SAMtools throughput sequencing data and Unix/Linux MIT
project
alignments in sam/bam format

Suite of tools for assembly,

Unix/Linux,
SOAP Suite alignment, and analysis of short read GPL BGI
macOS
next generation sequencing data

Sequence assembly, editing, and Wellcome Trust

Staden analysis, mainly consisting of gap4, Linux, macOS, Sanger Institute,
BSD
Package gap5, and spin. Written in C, C++, Windows Medical Research
Fortran and Tcl. Council
Taverna Tool to design and execute Linux, macOS,
LGPL myGrid
workbench workflows Windows

Inference, validation and Université du

T-REX (web Web browser,
visualization of phylogenetic trees ? Québec à
server) Windows
and phylogenetic networks Montréal

Integrated bioinformatics tools, Linux, macOS,

UGENE GPL 2 Unipro
written in C++ (Qt) Windows
Metaproteomics biodiversity
Unipept analysis written in Ruby and Web browser MIT Ghent University
JavaScript

Linux, macOS,
A Coarse-grained modeling package Max Planck
Windows, any Apache
VOTCA for molecular dynamics, written in Institute for
other Unix License 2.0
C++, Perl, BASH Polymer Research
variety

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 (http://www.biopython.org/DIST/LICENSE)
 2. "GeWorkbench License" (http://wiki.c2b2.columbia.edu/workbench/index.php/GeWorkbench
_License). geWorkbench. Columbia University. 15 June 2014.

External links
Free Biology Software (http://directory.fsf.org/category/bio/) – Free Software Directory – Free
Software Foundation

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