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BSML - Bioinformation Sequence Markup Language
Extensible language specification and container for bioinformatic data.
http://www.bsml.org/

BioPython.org
The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
http://biopython.org/

Bioperl.org
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.
http://www.bioperl.org

Public Domain Software in Biology
The aim of this project is to build the database of public domain software in biology and to distribute these software on-line as well as off-line. These computer software developed by people for people and are available free to potential users. The software collected on this site will be available on-line free for users via internet (e.g. FTP, Email Server, web browser ).
http://imtech.res.in/pdsb/

Bionconductor
The Bioconductor project produces an open source software framework that will assist biologists and statisticians working in bioinformatics, with primary emphasis on inference using DNA microarrays, built mostly using R.
http://www.bioconductor.org/