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- Blast
- Bioconductor
- Bioperl
- BioMart Perl APIs
- NCBI Eutils
- R
- Python Library
- Graphics programs
- BOOST libraries
- Phred, Phrap, Consed, cross_match, daev
- Hmmer
- Data compression programs
- Clustering programs - MCL and usearch/uclust
Microarray data analysis tools
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