The bio package

This is a collection of data structures and algorithms useful for building bioinformatics-related tools and utilities.

Current list of features includes: a Sequence data type supporting protein and nucleotide sequences and conversion between them. As of version 0.4, different kinds of sequence have different types. Support for quality data, reading and writing Fasta formatted files, reading TwoBit and phd formats, and Roche/454 SFF files. Rudimentary (i.e. unoptimized) support for doing alignments - including dynamic adjustment of scores based on sequence quality. Also 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.

Properties

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
Dependencies	array, base (4.), binary (0.4.), bytestring (≥0.9.1), containers, directory, mtl, old-time, parallel, parsec, process, QuickCheck (≥2), random, tagsoup (≥0.8)
License	LGPL
Author	Ketil Malde
Maintainer	ketil@malde.org
Category	Bioinformatics
Home page	http://biohaskell.org/Libraries/Bio
Source repository	darcs get http://malde.org/~ketil/biohaskell/biolib
Executables	frename, frecover, fastout, flx, qc
Upload date	Mon Mar 21 17:33:00 UTC 2011
Uploaded by	KetilMalde
Built on	ghc-7.0
Distributions	FreeBSD: 0.5.2

Modules

Bio

Downloads

bio-0.5.0.1.tar.gz (Cabal source package)
package description (included in the package)