The bio package
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.
- No changelog available
Properties
| 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) |
| License | LGPL |
| Author | Ketil Malde |
| Maintainer | ketil@ii.uib.no |
| Category | Bioinformatics |
| Home page | http://blog.malde.org/index.php/the-haskell-bioinformatics-library/ |
| Upload date | Fri Jan 30 19:28:09 UTC 2009 |
| Uploaded by | KetilMalde |
| Distributions | FreeBSD:0.5.2 |
| Downloads | 1120 total (140 in last 30 days) |
Modules
- Bio
- Alignment
- Bio.Clustering
- GFF3
- Location
- Bio.Sequence
- Bio.Util
Downloads
- bio-0.3.5.tar.gz [browse] (Cabal source package)
- Package description (included in the package)
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