bio: A bioinformatics library
This is a collection of data structures and algorithms useful for building bioinformatics-related tools and utilities.
Current list of features includes: a Sequence data type supporting protein and nucleotide sequences and conversion between them. As of version 0.4, different kinds of sequence have different types. Support for quality data, reading and writing Fasta formatted files, reading TwoBit and phd formats, and Roche/454 SFF files. Rudimentary (i.e. unoptimized) support for doing alignments - including dynamic adjustment of scores based on sequence quality. Also 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.
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Modules
[Index]
- Bio
- Alignment
- Bio.Alignment.AAlign
- Bio.Alignment.ACE
- Bio.Alignment.AlignData
- Bio.Alignment.BED
- Bio.Alignment.Blast
- Bio.Alignment.BlastData
- Bio.Alignment.BlastFlat
- Bio.Alignment.BlastXML
- Bio.Alignment.Bowtie
- Bio.Alignment.Matrices
- Bio.Alignment.Multiple
- Bio.Alignment.PSL
- Bio.Alignment.QAlign
- Bio.Alignment.SAlign
- Bio.Alignment.Soap
- Bio.Clustering
- GFF3
- Location
- Bio.Sequence
- Bio.Util
- Alignment
Flags
Automatic Flags
Name | Description | Default |
---|---|---|
test | Build testing software | Disabled |
examples | Build example programs | Enabled |
Use -f <flag> to enable a flag, or -f -<flag> to disable that flag. More info
Downloads
- bio-0.5.3.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
Maintainer's Corner
For package maintainers and hackage trustees
Candidates
- No Candidates
Versions [RSS] | 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 (>=4 && <5), binary (>=0.4 && <0.5), bytestring (>=0.9.1), containers, directory, mtl, old-time, parallel, parsec, process, QuickCheck (>=2), random, tagsoup (>=0.8) [details] |
Tested with | ghc ==7.6.2 |
License | LicenseRef-LGPL |
Author | Ketil Malde |
Maintainer | ketil@malde.org |
Category | Bioinformatics |
Home page | http://biohaskell.org/Libraries/Bio |
Source repo | head: darcs get http://malde.org/~ketil/biohaskell/biolib |
Uploaded | by KetilMalde at 2013-07-20T07:33:11Z |
Distributions | FreeBSD:0.5.3 |
Reverse Dependencies | 2 direct, 0 indirect [details] |
Executables | rselect-pe, orf, flowclip, frename, frecover, fastout, flx, qc |
Downloads | 14340 total (48 in the last 30 days) |
Rating | (no votes yet) [estimated by Bayesian average] |
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Status | Docs uploaded by user Build status unknown [no reports yet] |