The Bioperl Project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research. The Bioperl server provides an online resource for modules, scripts, and web links.

Bioinformation Sequence Markup Language. Extensible language specification and container for bioinformatic data.

Dynamite is a code generating language whose main purpose is to produce efficient code for dynamic programming. Dynamic programming is used throughout sequence analysis in a variety of different guises (sequence alignment, gene prediction etc). Dynamite is used extensively by myself (Ewan Birney), in particular for the Wise2 package.

OO Interface to AceDB

Java program to display a DNA sequence, annotated with features, ORFs. Reads many input formats.

The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.

The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.

The proBiosys suite of programs compares phenetic, chemotaxonomic and nucleic acid sequence data. Algorithms for polyphasic taxonomy are available to construct Dendrograms, the suite is simple to use.

The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprieatry systems like GCG.

AbOrygen develops the next generation of bioinformatics software with powerful new features that simplify and improve the research work of life scientists worldwide.