bio: A bioinformatics library
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/biohaskell/biolib.
| Versions | 0.3.3, 0.3.3.1, 0.3.3.2, 0.3.3.4 |
|---|---|
| Dependencies | array, base (>3), binary, bytestring, containers, 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/ |
| Upload date | Wed Jul 31 05:08:49 UTC 2008 |
| Uploaded by | KetilMalde |
| Built on | ghc-6.10, ghc-6.8 |
Modules
- Bio
- Alignment
- Bio.Clustering
- Bio.Sequence
- Bio.Util
Downloads
- bio-0.3.3.4.tar.gz (Cabal source package)
- package description (included in the package)