| 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
|
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
|
| 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
|
| 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
|
