Мы используем файлы cookie.
Продолжая использовать сайт, вы даете свое согласие на работу с этими файлами.
Продолжая использовать сайт, вы даете свое согласие на работу с этими файлами.
List of open-source bioinformatics software
List of open-source bioinformatics software
Подписчиков: 0, рейтинг: 0
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 |
---|---|---|---|---|
.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 | 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 | 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 |
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