The bio package

[ Tags: bioinformatics, lgpl, library ] [ Propose Tags ]

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.


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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]
License LGPL
Author Ketil Malde
Maintainer ketil@ii.uib.no
Category Bioinformatics
Home page http://blog.malde.org/index.php/the-haskell-bioinformatics-library/
Uploaded Tue Jun 16 10:30:47 UTC 2009 by KetilMalde
Distributions FreeBSD:0.5.3, NixOS:0.5.3
Downloads 5488 total (556 in the last 30 days)
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Readme for bio-0.4

[back to package description]
biolib - a Haskell library for bioinformatics

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.

To install, you need to acquire a working GHC (possibly other Haskell
system).  You also need the following external libraries:

  QuickCheck   - for unit tests
  binary       - mainly for dealing with the TwoBit sequence format
  tagsoup      - for parsing XML output from Blast

You should be able to get what you need from <http://hackage.haskell.org/>.

You can then build with 'make', doing either 'make install' if you can sudo, or 'make user_install' if you can not.  Of course, the Makefile just proxies for
the regular Cabal routine, which will work just as well:

    runhaskell Setup configure
    runhaskell Setup build
    sudo runhaskell Setup install

(Use --prefix=$HOME and remove the sudo, if you don't want to install as root.)

If that didn't work, mail me at <ketil@malde.org>, and we'll try to
work things out.