| Software | Description | Resources | Platform | License | Developer |
|---|
| .NET Bio | A language-neutral bioinformatics toolkit built using the Microsoft 4.0 .NET Framework to help developers, researchers, and scientists. | Website | .NET Framework | Apache License | Collaborative project |
| Anduril | Component-based workflow framework for data analysis | Website | Linux, Mac OS X, Windows | GPL | University of Helsinki |
| Armadillo workflow platform | Tool for designing and executing phylogenetic workflows | Website | Mac OS X, Windows | General Public Licence (GPL) | Armadillo |
| AutoDock | suite of automated docking tools | Website | Platform | GNU GPL | Developer |
| Biochemical Algorithms Library (BALL) | C++ library and framework for molecular modeling and visualization designed for rapid prototyping | Website – Articles | 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 | Website | Cross-platform | GPL v3 | Oh no sequences! |
| Bioclipse | Visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). | Website | Platform | Eclipse Public License | The Bioclipse Project |
| Bioconductor | R (programming language) language toolkit | Website – Articles | 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 | Project Home – Download for Windows | Windows (stand-alone), Linux & Mac OS X (source code only with Qt libraries) | Academic Free License | Collaborative project |
| BioHaskell | Haskell (programming language) | Project web site – Bioinformatics software in Haskell | Linux, Mac OS X, Windows | GPL, LGPL, and BSD | Collaborative project |
| BioJava | Java (programming language) | Website | Linux, Mac OS X, Windows | LGPL v2.1 | Open Bioinformatics Foundation |
| BioMOBY | registry of web services | Website – Articles | Web | License | Open Bioinformatics Foundation |
| BioPerl | Perl language toolkit | Website | Cross-platform | Artistic License & GPL | Open Bioinformatics Foundation |
| BioPHP | PHP language toolkit | Website | Platform | License | Open Bioinformatics Foundation |
| Biopython | Python language toolkit | Website | Cross-platform | Biopython License | Open Bioinformatics Foundation |
| BioRails | a data management system designed to support researchers in drug discovery | Website | Platform | License | Developer |
| BioRuby | Ruby language toolkit | Website | Platform | GNU GPL v2 or Ruby license | Open Bioinformatics Foundation |
| BioSmalltalk | Smalltalk language toolkit | Website | 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. | Website | Cross-platform | MIT license | TupiLabs |
| caCORE | ontologic representation environment | Website – Articles | Platform | License | National Cancer Institute |
| caArray | ontologic representation environment | [1] – [2] | Platform | License | National Cancer Institute |
| EMBOSS | Suite of packages for sequencing, searching, etc. | Website | Platform | General Public Licence (GPL) and Library GPL | Collaborative project |
| Gaggle | A framework for interoperability between systems biology software | Website – Paper – Firegoose paper | Linux, Mac OS X, Windows | LGPL | Institute for Systems Biology |
| Galaxy | Scientific workflow and data integration system | Website | Unix-like | License | Penn State and Emory University |
| GenePattern | Scientific workflow system that provides access to more than 150 genomic analysis tools | Website | Unix-like (public server); Linux, Mac OS X, Windows | MIT license | Broad Institute |
| GMOD | Toolkit for addressing many common challenges at biological databases. | Website | Unix-like (server), Web browser (client) | Varies depending on tool | Collaborative project |
| GenGIS | Application that allows users to combine digital map data with information about biological sequences collected from the environment. | Website | Windows, Mac OS X | GPL | Collaborative project |
| GenomeSpace | Centralized web application that provides data format transformations and facilitates connections with other bioinformatics tools | Website | Web browser | LGPL | Broad Institute, Collaborative project |
| GENtle | An equivalent to the proprietary Vector NTI, a tool to analyze and edit DNA sequence files | Website | Platform | GPL | Magnus Manske |
| Integrated Genome Browser | Java-based desktop genome browser | Website | 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 | Website | Linux, Mac OS X, Windows | LGPL | Broad Institute |
| IntAct | molecular interaction database | Website – Articles | Platform | License | European Bioinformatics Institute |
| InterMine | Extensive data warehouse system for the analysis and integration of biological datasets | Website | Cross-platform | LGPL | University of Cambridge |
| Java Treeview | microarray data viewer | Website – Articles | Cross-platform | License | Developer |
| LabKey Server | platform for integrating, analyzing and sharing data | Website | Linux, Mac OS X, Windows | Apache License | LabKey Software Foundation |
| OpenClinica | software for capturing and managing data in clinical trials | Website | Linux, Windows | LGPL | OpenClinica |
| PromKappa | PromKappa (Promoter analysis by Kappa) software program used for promoter pattern generation and promoter analysis. | Download here. | Windows | Open access | University of Bucharest |
| MeV: Multi-Experiment Viewer | a desktop application for the analysis, visualization and data-mining of large-scale genomic data | website | Linux, Mac OS X, Windows | Artistic License | Dana-Farber Cancer Institute |
| REDCRAFT | software for determining tertiary protein structure given assigned Residual Dipolar Coupling data | Website | Linux, Mac OS X, Windows | GPL v3 | REDCRAFT |
| SAM Tools | Data format (SAM) and accompanying tool suite, for storing large nucleotide sequence alignments | Website | Linux | BSD, MIT License | 1000 Genomes Project |
| Staden Package | Sequence assembly, editing and analysis, primarily consisting of gap4, gap5 and spin. | Website | 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. | Website | Windows, Mac OS X | GPL | Collaborative project |
| Taverna workbench | Tool for designing and executing workflows | Website | Linux, Mac OS X, Windows | LGPL | myGrid |
| T-REX WebServer | Bioinformatics and phylogenetics webserver (NJ, PhyML, RAxML, MAFFT, MUSCLE, Newick viewer, Horizontal gene transfer detection, Reticulograms, Substitution models) | Website | Web platform | Academic Free License | T-REX |
| UGENE | integrated bioinformatics tools | Website – Podcast | Linux, Mac OS X, Windows | GPL2 License | Unipro |
| Visomics | bioinformatics tools for omics data | Website | Windows | Apache 2.0 License | Collaborative Project |
