The bio package

[Tags: lgpl, library]

This is a collection of data structures and algorithms I've found useful when building various bioinformatics-related tools and utilities.

Current list of features includes: a Sequence data type supporting protein and nucleotide sequences and conversion between them, quality data, reading and writing Fasta formatted files, reading TwoBit and phd formats. Rudimentary support for doing alignments - including dynamic adjustment of scores based on sequence quality - and Blast output parsing. Partly implemented single linkage clustering, and multiple alignment.

The Darcs repository is at:


Versions0.3.3,,,, 0.3.5, 0.4, 0.4.4, 0.4.5, 0.4.6, 0.4.7, 0.4.8, 0.5,, 0.5.1, 0.5.2, 0.5.3
Dependenciesarray, base (>3), binary, bytestring, containers, parallel, parsec, QuickCheck (<2), tagsoup (>=0.4)
AuthorKetil Malde
Home page
Upload dateWed Mar 12 09:16:24 UTC 2008
Uploaded byKetilMalde
Downloads1385 total (119 in last 30 days)




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