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bio: A bioinformatics library

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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 [faq] 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 LicenseRef-LGPL
Author Ketil Malde
Maintainer ketil@ii.uib.no
Category Bioinformatics
Home page http://blog.malde.org/index.php/the-haskell-bioinformatics-library/
Uploaded by KetilMalde at Fri Jan 30 19:28:09 UTC 2009
Distributions FreeBSD:0.5.3, NixOS:0.5.3
Downloads 8211 total (245 in the last 30 days)
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Readme for bio-0.3.5

[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.