Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development.
A community effort to produce Perl code for application in biology
Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP)
Access to Biological Web Services from Python
Open-source project dedicated to providing a Java framework for processing biological data.
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
(Max-Planck Institute for Developmental Biology)
The Bioinformatic Toolkit is a platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house, and serveral public tools are offered with extended functionality.
NCBI Genome Workbench
(National Center for Biotechnology Information (US))
NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.
(.NET Bio Community (Open Source))
.NET Bio (formerly Microsoft Biology Foundation [MBF]) is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework—initially aimed at the area of Genomics research.
Microsoft Biology Tools
The Microsoft Biology Tools (MBT) are a collection of tools that enable biology and bioinformatics researchers to be more productive in making scientific discoveries. Some of the tools provided here take advantage of the capabilities of .NET Bio (formerly Microsoft Biology Foundation), and are good examples of how you can use .NET Bio to create other tools.
(European Bioinformatics Institute)
The HMMER web server: fast and sensitive homology searches.