Commercial sequence analysis and manipulation suite for Windows and Macintosh.

A hierarchical database system for displaying genomic data (originally C. elegans), suitable also for displaying other scientific data.

Bioinformatics programs, including MendelBase.

C++ framework for rapid software prototyping in molecular modeling.

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.