The bio package (version 0.3.3.1)
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.
| Other versions | 0.3.3, 0.3.3.2 |
|---|---|
| Dependencies | array, base (>3), binary, bytestring, containers, interlude, parallel, parsec, QuickCheck (<2), tagsoup (>=0.4) |
| License | LGPL |
| Author | Ketil Malde |
| Maintainer | ketil@ii.uib.no |
| Category | Bioinformatics |
| Home page | http://malde.org/~ketil/ |
| Exposed modules | Bio.Sequence, Bio.Sequence.SeqData, Bio.Sequence.Fasta, Bio.Sequence.TwoBit, Bio.Sequence.Phd, Bio.Sequence.Entropy, Bio.Sequence.HashWord, Bio.Sequence.GOA, Bio.Alignment.BlastData, Bio.Alignment.BlastFlat, Bio.Alignment.Blast, Bio.Alignment.BlastXML, Bio.Alignment.AlignData, Bio.Alignment.Matrices, Bio.Alignment.SAlign, Bio.Alignment.AAlign, Bio.Alignment.QAlign, Bio.Alignment.Multiple, Bio.Alignment.ACE, Bio.Clustering, Bio.Util, Bio.Util.Parsex |
| Upload date | Tue Mar 11 07:59:06 PDT 2008 |
| Uploaded by | KetilMalde |
| Build failure | ghc-6.8 (log) |
Downloads
- bio-0.3.3.1.tar.gz (Cabal source package)
- package description (included in the package)