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The National Cancer Institute's Center for Bioinformatics produces the caCORE infrastructure, an open-source enterprise architecture for cancer informatics.
An open source library of Java bioinformatics algorithms. The current version consists mainly of sequence alignment algorithms such as Needleman- Wunsch and Smith-Waterman.
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.
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.