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/bio.
| Versions | 0.3.3, 0.3.3.1, 0.3.3.2, 0.3.3.4, 0.3.5, 0.4 |
|---|---|
| Dependencies | array, base (>3), binary, bytestring, containers, interlude, parallel, parsec, QuickCheck (<2), tagsoup (>=0.5) |
| License | LGPL |
| Author | Ketil Malde |
| Maintainer | ketil@ii.uib.no |
| Category | Bioinformatics |
| Home page | http://malde.org/~ketil/ |
| Upload date | Tue Mar 4 20:02:42 UTC 2008 |
| Uploaded by | GwernBranwen |
| Build failure | ghc-6.10 (log), ghc-6.8 (log) |
Modules
- Bio
- Alignment
- Bio.Alignment.AAlign
- Bio.Alignment.ACE
- Bio.Alignment.AlignData
- Bio.Alignment.Blast
- Bio.Alignment.BlastData
- Bio.Alignment.BlastFlat
- Bio.Alignment.BlastXML
- Bio.Alignment.Matrices
- Bio.Alignment.Multiple
- Bio.Alignment.QAlign
- Bio.Alignment.SAlign
- Bio.Clustering
- Bio.Sequence
- Bio.Sequence.Entropy
- Bio.Sequence.Fasta
- Bio.Sequence.GOA
- Bio.Sequence.HashWord
- Bio.Sequence.Phd
- Bio.Sequence.SeqData
- Bio.Sequence.TwoBit
- Bio.Util
- Bio.Util.Parsex
- Alignment
Downloads
- bio-0.3.3.tar.gz (Cabal source package)
- package description (included in the package)