The bio package
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. Reading Gene Ontology (GO) annotations (GOA) and definitions/hierarchy.
The Darcs repository is at: http://malde.org/~ketil/biohaskell/biolib.
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|Versions||0.3.3, 0.3.3.1, 0.3.3.2, 0.3.3.4, 0.3.5, 0.4, 0.4.4, 0.4.5, 0.4.6, 0.4.7, 0.4.8, 0.5, 0.5.0.1, 0.5.1, 0.5.2, 0.5.3|
|Dependencies||array, base (>3), binary, bytestring (>=0.9.1), containers, mtl, old-time, parallel, parsec, QuickCheck (<2), random, tagsoup (>=0.4) [details]|
|Uploaded||Fri Jan 30 19:28:09 UTC 2009 by KetilMalde|
|Downloads||4154 total (38 in the last 30 days)|
|Status||Docs uploaded by user
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