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.
| 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 | Apache | Collaborative project |
| AMPHORA
| Metagenomics analysis software | Linux | GPL |
| Anduril
| Component-based workflow framework for data analysis | GPL |
| Apache Taverna
| Written in Java | Apache License 2.0 |
| 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 |
| Avogadro
| C++ (Qt) based molecule editor and visualizer for in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. | 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 | The Bioclipse Project |
| Bioconductor
| R (programming language) language toolkit | Artistic 2.0 |
| 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 | LGPL v2.1 |
| BioJS
| JavaScript library of components to visualize biological data | Apache | [http://blog.biojs.net/aboutme/ BioJS Community] |
| BioMOBY
| Registry of web services | Artistic |
| BioPerl
| Perl language toolkit |
| BioPHP
| PHP language toolkit with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools | GPL v2 |
| Biopython
| Python language toolkit | Biopython[http://www.biopython.org/DIST/LICENSE Biopython License] |
| 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 }} |
| BLAST
| Algorithm and program for comparing primary biological sequence information, including DNA and protein sequences. |
| CP2K
| Perform atomistic simulations of solid state, liquid, molecular and biological systems, written in Fortran 2003. | 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 }} | Collaborative project |
| Galaxy
| Scientific workflow and data integration system | Collaborative project |
| GenePattern
| Scientific workflow system that provides access to hundreds of genomic analysis tools | Unix-like (public server); Linux, macOS, Windows | MIT |
| Geworkbench
| Genomic data integration platform | 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 }} |
| 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 | GPL | Collaborative project |
| GenoCAD
| A computer-assisted design (CAD) tool for synthetic biology, used to design genetic constructs based on grammar rules. | 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 | LGPL | Broad Institute, collaborative project |
| GENtle
| An equivalent to the proprietary Vector NTI, a tool to analyze and edit DNA sequence files | GPL |
| gget
| Efficient querying of genomic reference databases including UniProt, National Center for Biotechnology Information, and Ensembl genome database project | BSD | Laura Luebbert and Lior Pachter |
| GROMACS
| Molecular dynamics package mainly designed for simulations of proteins, lipids and nucleic acids. | Common Public 1.0 | GenoViz |
| Integrated Genome Browser
| Java-based desktop genome browser | Common Public 1.0 | GenoViz |
| InterMine
| Extensive data warehouse system for the analysis and integration of biological datasets written in Java and JavaScript | LGPL |
| LabKey Server
| Software platform, allows organizations to integrate, analyze, and share complex biomedical data | Apache | LabKey Software Foundation |
| LAMMPS
| Molecular dynamics program written in C++ | Apache | Sandia National Laboratories. |
| mothur
| Software for analysis of 16S rRNA gene amplicon sequence data | GPL |
| Nextflow
| A workflow management system used for building and running scalable and reproducible bioinformatics pipelines, especially in cloud and high-performance computing environments. | Apache License 2.0 |
| PathVisio
| Desktop software for drawing, analyzing, and visualizing biological pathways | Apache 2.0 |
| 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 | GPL |
| SAMtools
| Utilities for interacting with high-throughput sequencing data and alignments in sam/bam format | MIT | Collaborative project |
| SOAP Suite
|Suite of tools for assembly, alignment, and analysis of short read next generation sequencing data |GPL |BGI |
| Staden Package
| Sequence assembly, editing, and analysis, mainly consisting of gap4, gap5, and spin. Written in C, C++, Fortran and Tcl. | BSD |
| Taverna workbench
| Tool to design and execute workflows | LGPL | myGrid |
| T-REX (web server)
| Inference, validation and visualization of phylogenetic trees and phylogenetic networks | GNU (GPL) v3 |
| UGENE
| Integrated bioinformatics tools, written in C++ (Qt) | GPL 2 | Unipro |
| Unipept
| Metaproteomics biodiversity analysis written in Ruby and JavaScript | MIT |
| VOTCA
| A Coarse-grained modeling package for molecular dynamics, written in C++, Perl, BASH | Linux, macOS, Windows, any other Unix variety | 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
{{Reflist}}
External links
- [http://directory.fsf.org/category/bio/ Free Biology Software] – Free Software Directory – Free Software Foundation
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