bio-0.3.3.1: A bioinformatics library

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.

The Darcs repository is at: http://malde.org/~ketil/bio.

Properties

Versions0.3.3, 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
Dependenciesarray, base (>3), binary, bytestring, containers, interlude, parallel, parsec, QuickCheck (<2), tagsoup (≥0.4)
LicenseLGPL
AuthorKetil Malde
Maintainerketil@ii.uib.no
CategoryBioinformatics
Home pagehttp://malde.org/~ketil/
Upload dateTue Mar 11 14:59:06 UTC 2008
Uploaded byKetilMalde
Build failureghc-6.10 (log), ghc-6.12 (log), ghc-6.8 (log), ghc-7.4 (log)
DistributionsFreeBSD: 0.5.2

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