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.

Software  | Description  | Platform  | License  | Developer

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.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
cBioPortal | cBioPortal's primary goal is to make complex cancer genomic data accessible and interpretable for cancer biologists and clinicians by transforming multimodal data into interactive visualizations that facilitate biological discovery and clinical decision-making.  | Web browser | AGPL | cBioPortal community
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
Tracer  | Open-source eBPF-based observability client for monitoring performance and resource usage in bioinformatics workflows.  | Linux | Custom license (see GitHub)  | Tracer Project GitHub
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

* Comparison of software for molecular mechanics modeling
* Earth BioGenome Project
* 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
* List of proprietary bioinformatics software

## References

1. ↑ "(PDF) Bioclipse: An open source workbench for chemo- and bioinformatics". https://www.researchgate.net/publication/6490579_Bioclipse_An_open_source_workbench_for_chemo-_and_bioinformatics.
2. ↑ Biopython License
3. ↑ Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki (2010). "BioRuby: Bioinformatics software for the Ruby programming language". Bioinformatics 26 (20): 2617–2619. doi:10.1093/bioinformatics/btq475. PMID 20739307. PMC 2951089. https://academic.oup.com/bioinformatics/article/26/20/2617/194139#.
4. ↑ "EMBOSS Downloads". https://emboss.sourceforge.net/download/.
5. ↑ "GeWorkbench License". Columbia University. 15 June 2014. http://wiki.c2b2.columbia.edu/workbench/index.php/GeWorkbench_License.
6. ↑ "Empowering Scientific Research with Nextflow + AI". 3 December 2024. https://www.genengnews.com/sponsored/empowering-scientific-research-with-nextflow-ai/.
7. ↑ "Trex-online". http://www.trex.uqam.ca/.

## External links

* Free Biology Software – Free Software Directory – Free Software Foundation

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