| 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 |
| AutoDock |
Suite of automated docking tools |
? |
GPL |
? |
| Biochemical Algorithms Library (BALL) |
C++ library and framework for molecular modeling and visualization designed for rapid prototyping |
Linux, macOS, Windows |
LGPL |
BALL project team |
| 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 |
Linux, macOS, Windows |
LGPL v2.1 |
Open Bioinformatics Foundation |
| BioJS |
JavaScript |
Web browser |
Apache |
? |
| BioJulia |
Julia |
Linux, macOS, Windows |
MIT License |
BioJulia Bioinformatics and Computational Biology in Julia |
| 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 |
? |
GPL v2 |
Open Bioinformatics Foundation |
| Biopython |
Python language toolkit |
Cross-platform |
Biopython[1] |
Open Bioinformatics Foundation |
| BioRuby |
Ruby language toolkit |
? |
GPL v2 or Ruby |
Open Bioinformatics Foundation |
| EMBOSS |
Suite of packages for sequencing, searching, etc. |
? |
GPL and LGPL |
Collaborative project |
| Galaxy |
Scientific workflow and data integration system |
Unix-like |
Academic Free |
Pennsylvania State University and Emory University |
| GenePattern |
Scientific workflow system that provides access to more than 150 genomic analysis tools |
Unix-like (public server); Linux, macOS, Windows |
MIT |
Broad Institute |
| Geworkbench |
Genomic data integration platform |
Linux, macOS, Windows |
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 |
| 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 |
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 |
| mothur |
Software for analysis of the 16S rRNA gene |
Linux, macOS, Windows |
|
University of Michigan |
| PathVisio |
Desktop software for drawing, analysing, and visualizing biological pathways |
Linux, macOS, Windows |
Apache 2.0 |
Maastricht University |
| Orange |
Component-based data mining and machine learning software suite, 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 |
| Staden Package |
Sequence assembly, editing, and analysis, mainly consisting of gap4, gap5, and spin. |
Linux, macOS, Windows |
BSD |
Wellcome Trust Sanger Institute, Medical Research Council |
| Taverna workbench |
Tool to design and execute workflows |
Linux, macOS, Windows |
LGPL |
myGrid |
| UGENE |
Integrated bioinformatics tools |
Linux, macOS, Windows |
GPL 2 |
Unipro |
| Unipept |
Metaproteomics biodiversity analysis |
Web browser |
MIT |
Ghent University |
