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 .
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 , and we'll try to
work things out.