BiobaseInfernal: Infernal data structures and tools
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Warnings:
- 'ghc-options: -O2' is rarely needed. Check that it is giving a real benefit and not just imposing longer compile times on your users.
- Exposed modules use unallocated top-level names: Biobase
Provides import and export facilities for Infernal/Rfam data formats. We include Stockholm, CM, verbose Infernal results, and tabulated Infernal results. Some small tools are included.
The VerboseHit format is slightly extended to allow simple annotations. This extension should be backward-compatible with standard-compliant parsers.
The cmsearchFilter program provides filtering and coloring
options.
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Properties
| Versions | 0.0.2.0, 0.0.2.1, 0.5.0.0, 0.5.1.0, 0.5.2.0, 0.5.3.0, 0.5.3.1, 0.5.4.0, 0.5.4.1, 0.6.0.0, 0.6.0.1, 0.6.2.0, 0.7.0.0, 0.7.0.1, 0.7.1.0, 0.8.1.0, 0.8.1.0 |
|---|---|
| Change log | changelog.md |
| Dependencies | aeson (>=0.9), attoparsec (>=0.12), base (>=4.7 && <5.0), binary (>=0.7), BiobaseInfernal, BiobaseTypes (>=0.1.2 && <0.1.3), BiobaseXNA (>=0.9.3 && <0.9.4), bytestring, cereal (>=0.4), cereal-text (>=0.1), cereal-vector (>=0.2), cmdargs (>=0.10), containers, data-default (>=0.5), deepseq (>=1.4), DPutils (>=0.0.1 && <0.0.2), filepath (>=1.3), hashable (>=1.2), lens (>=4.0), parallel (>=3.0), pipes (>=4.0), pipes-attoparsec (>=0.5), pipes-bytestring (>=2.0), pipes-parse (>=3.0), pipes-safe (>=2.2), pipes-zlib (>=0.4), primitive (>=0.5), PrimitiveArray (>=0.8.0 && <0.8.1), strict (>=0.3), string-conversions (>=0.4), text (>=1.0), text-binary (>=0.1), transformers, tuple (>=0.3), unordered-containers (>=0.2), utf8-string (>=1.0), vector (>=0.10), vector-th-unbox (>=0.2), zlib (>=0.6) [details] |
| License | GPL-3.0-only |
| Copyright | Christian Hoener zu Siederdissen, 2011 - 2017 |
| Author | Christian Hoener zu Siederdissen |
| Maintainer | choener@bioinf.uni-leipzig.de |
| Category | Bioinformatics |
| Home page | https://github.com/choener/BiobaseInfernal |
| Bug tracker | https://github.com/choener/BiobaseInfernal/issues |
| Source repo | head: git clone git://github.com/choener/BiobaseInfernal |
| Uploaded | by ChristianHoener at 2017-03-14T13:57:16Z |
Modules
- Biobase
- SElab
- Biobase.SElab.CM
- Biobase.SElab.CM.Import
- Biobase.SElab.CM.ModelStructure
- Biobase.SElab.CM.Types
- Common
- Biobase.SElab.Common.Parser
- Biobase.SElab.HMM
- Biobase.SElab.HMM.Import
- Biobase.SElab.HMM.Types
- Biobase.SElab.Model
- Biobase.SElab.Model.Import
- Biobase.SElab.Model.Types
- Biobase.SElab.Taxonomy
- Biobase.SElab.Taxonomy.Import
- Biobase.SElab.CM
- SElab
Downloads
- BiobaseInfernal-0.8.1.0.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
Maintainer's Corner
Package maintainers
For package maintainers and hackage trustees
Readme for BiobaseInfernal-0.8.1.0
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BiobaseInfernal
Low-level handling of Infernal file formats. Appropriate efficient Haskell data structures for high-performance computations with Infernal covariance models.
In particular, the _states structure provides a numerics-friendly interface to the actual model.
Contact
Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany
choener@bioinf.uni-leipzig.de
http://www.bioinf.uni-leipzig.de/~choener/