List of open-source bioinformatics software

{{Short description|None}}

This is a list of computer software which is made for bioinformatics and released under open-source software licenses with articles in Wikipedia.

class="wikitable sortable"
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

| [https://www.openchemistry.org/projects/ Open Chemistry Project]

BEDtools

| "Genome arithmetic"—manipulation of coordinate sets and the extraction of sequences from a BED file.

| Linux

| MIT

| [http://quinlanlab.org/ QuinlanLab], University of Utah

Bioclipse

| Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP)

| Linux, macOS, Windowshttps://www.researchgate.net/publication/6490579_Bioclipse_An_open_source_workbench_for_chemo-_and_bioinformatics

| 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

| [http://blog.biojs.net/aboutme/ 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[http://www.biopython.org/DIST/LICENSE Biopython License]

| Open Bioinformatics Foundation

BioRuby

| Ruby language toolkit

| Linux, macOS, Windows{{cite journal | url=https://academic.oup.com/bioinformatics/article/26/20/2617/194139# | doi=10.1093/bioinformatics/btq475 | title=BioRuby: Bioinformatics software for the Ruby programming language | date=2010 | last1=Goto | first1=Naohisa | last2=Prins | first2=Pjotr | last3=Nakao | first3=Mitsuteru | last4=Bonnal | first4=Raoul | last5=Aerts | first5=Jan | last6=Katayama | first6=Toshiaki | journal=Bioinformatics | volume=26 | issue=20 | pages=2617–2619 | pmid=20739307 }}

| 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{{cite web | url=https://emboss.sourceforge.net/download/ | title=EMBOSS Downloads }}

| 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{{cite web |title=GeWorkbench License |date=15 June 2014 |website=geWorkbench |publisher=Columbia University |url=http://wiki.c2b2.columbia.edu/workbench/index.php/GeWorkbench_License }}

| 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{{cite web | url=https://www.genengnews.com/sponsored/empowering-scientific-research-with-nextflow-ai/ | title=Empowering Scientific Research with Nextflow + AI | date=3 December 2024 }}

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 Montréalhttp://www.trex.uqam.ca/

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

References

{{Reflist}}