| NET Bio |
A language-neutral bioinformatics toolkit built using the Microsoft 4.0 .NET Framework to help developers, researchers, and scientists. |
.NET Framework |
Apache License |
Collaborative project |
| AMPHORA |
Metagenomics analysis software |
Linux |
GNU General Public License |
Developer |
| Anduril |
Component-based workflow framework for data analysis |
Linux, Mac OS X, Windows |
GPL |
University of Helsinki |
| Armadillo workflow platform |
Tool for designing and executing phylogenetic workflows |
Mac OS X, Windows |
General Public Licence (GPL) |
Armadillo |
| AutoDock |
suite of automated docking tools |
Platform |
GNU GPL |
Developer |
| Biochemical Algorithms Library (BALL) |
C++ library and framework for molecular modeling and visualization designed for rapid prototyping |
Linux, Mac OS X, Windows |
LGPL |
BALL project team |
| Bio4j |
Bio4j is a bioinformatics platform and graph based database built around most data available in UniProt KB(Swiss-Prot + TrEMBL), Gene Ontology (GO), UniRef (50,90,100), RefSeq, NCBI taxonomy, and Expasy Enzyme DB |
Cross-platform |
AGPL v3 |
Oh no sequences! |
| Bioclipse |
Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). |
Platform |
Eclipse Public License |
The Bioclipse Project |
| Bioconductor |
R (programming language) language toolkit |
Linux, Mac OS X, Windows |
Artistic License 2.0 |
Fred Hutchinson Cancer Research Center |
| Bioinformatics Learning Tutorial (BLT) |
Educational interactive tutorials and 3D animations for Replication, Transcription, and Translation |
Windows (stand-alone), Linux & Mac OS X (source code only with Qt libraries) |
Academic Free License |
Collaborative project |
| BioHaskell |
Haskell (programming language) |
Linux, Mac OS X, Windows |
GPL, LGPL, and BSD |
Collaborative project |
| BioJava |
Java (programming language) |
Linux, Mac OS X, Windows |
LGPL v2.1 |
Open Bioinformatics Foundation |
| BioMOBY |
registry of web services |
Web |
Artistic License |
Open Bioinformatics Foundation |
| BioPerl |
Perl language toolkit |
Cross-platform |
Artistic License & GPL |
Open Bioinformatics Foundation |
| BioPHP |
PHP language toolkit |
Platform |
GPL v2 |
Open Bioinformatics Foundation |
| Biopython |
Python language toolkit |
Cross-platform |
Biopython License |
Open Bioinformatics Foundation |
| BioRuby |
Ruby language toolkit |
Platform |
GNU GPL v2 or Ruby license |
Open Bioinformatics Foundation |
| BioSmalltalk |
Smalltalk language toolkit |
Cross-platform |
MIT license |
Developer |
| BioUno |
BioUno is a project that applies Continuous Integration tools and techniques in Bioinformatics. It uses Jenkins and its plug-in API to create biology workflows and manage computer clusters. |
Cross-platform |
MIT license |
TupiLabs |
| dnet |
An open-source R package for analysing biological networks and high-throughput biological data in an integrative manner |
Linux, Mac OS X, Windows |
GPL |
University of Bristol |
| EMBOSS |
Suite of packages for sequencing, searching, etc. |
Platform |
General Public Licence (GPL) and Library |
GPL Collaborative project |
| Gaggle |
A framework for interoperability between systems biology software |
Linux, Mac OS X, Windows |
LGPL |
Institute for Systems Biology |
| Galaxy |
Scientific workflow and data integration system |
Unix-like |
Academic Free License |
Penn State and Emory University |
| GenePattern |
Scientific workflow system that provides access to more than 150 genomic analysis tools |
Unix-like (public server); Linux, Mac OS X, Windows |
MIT license |
Broad Institute |
| GeWorkbench |
Genomic data integration platform |
Linux, Mac OS X, Windows |
License |
Columbia University |
| GMOD |
Toolkit for addressing many common challenges at biological databases. |
Unix-like (server), Web browser (client) |
Varies depending on tool |
Collaborative project |
| GeneProf |
A web-based, bioinformatics software suite for the analysis of functional genomics experiments, e.g. RNA-seq or ChIP-seq. |
Web browser |
Varies depending on tool |
Scottish Centre for Regenerative Medicine bioinformatics group |
| GenGIS |
Application that allows users to combine digital map data with information about biological sequences collected from the environment. |
Windows, Mac OS X |
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 |
Platform |
GPL |
Magnus Manske |
| Integrated Genome Browser |
Java-based desktop genome browser |
Linux, Mac OS X, Windows |
CPL 1.0 |
GenoViz |
| Integrative Genomics Viewer (IGV) |
High-performance desktop tool for interactive visual exploration of diverse genomic data |
Linux, Mac OS X, Windows |
LGPL |
Broad Institute |
| IntAct |
molecular interaction database |
Platform |
Apache License v2 |
European Bioinformatics Institute |
| InterMine |
Extensive data warehouse system for the analysis and integration of biological datasets |
Cross-platform |
LGPL |
University of Cambridge |
| Java Treeview |
microarray data viewer |
Cross-platform |
License |
Developer |
| LabKey Server |
platform for integrating, analyzing and sharing data |
Linux, Mac OS X, Windows |
Apache License |
LabKey Software Foundation |
| OpenClinica |
software for capturing and managing data in clinical trials |
Linux, Windows |
LGPL |
OpenClinica |
| PromKappa] |
PromKappa (Promoter analysis by Kappa) software program used for promoter pattern generation and promoter analysis. |
Windows |
Open access |
University of Bucharest |
| Multi-Experiment Viewer (MeV) |
a desktop application for the analysis, visualization and data-mining of large-scale genomic data |
Linux, Mac OS X, Windows |
Artistic License |
Dana-Farber Cancer Institute |
| PathVisio |
a desktop software for drawing, analysis and visualization of biological pathways |
Linux, Mac OS X, Windows |
Apache 2.0 License |
Maastricht University |
| REDCRAFT |
software for determining tertiary protein structure given assigned Residual Dipolar Coupling data |
Linux, Mac OS X, Windows |
GPL v3 |
REDCRAFT |
| SAM Tools |
Data format (SAM) and accompanying tool suite, for storing large nucleotide sequence alignments |
Linux |
BSD, MIT License |
1000 Genomes Project |
| Staden Package |
Sequence assembly, editing and analysis, primarily consisting of gap4, gap5 and spin. |
Linux, Mac OS X, Windows |
BSD |
Wellcome Trust Sanger Institute / Medical Research Council |
| STAMP |
Software package for analyzing metagenomic profiles that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. |
Windows, Mac OS X |
GPL |
Collaborative project |
| supraHex |
An open-source R/Bioconductor package for omics data analysis using a supra-hexagonal map |
Linux, Mac OS X, Windows |
GPL |
University of Bristol |
| Taverna workbench |
Tool for designing and executing workflows |
Linux, Mac OS X, Windows |
LGPL |
myGrid |
| TGAC Browser |
Genome Browser, visualisation solutions for big data in the genomic era |
Unix-like (server), Web browser (client) |
GPL V3 |
The Genome Analysis Centre (TGAC), UK |
| T-REX WebServer |
Bioinformatics and phylogenetics webserver (NJ, PhyML, RAxML, MAFFT, MUSCLE, Newick viewer, Horizontal gene transfer detection, Reticulograms, Substitution models) |
Web platform |
Academic Free License |
T-REX |
| UGENE |
integrated bioinformatics tools |
Linux, Mac OS X, Windows |
GPL2 |
Unipro |
| Visomics |
bioinformatics tools for omics data |
Windows |
Apache 2.0 License |
Collaborative Project |
| Genome Analysis Toolkit 1.0 (GATK 1.0) |
a software package to analyse next-generation resequencing data |
Linux |
MIT license |
Broad Institute |
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