BiobaseInfernal: Infernal data structures and tools

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Warnings:

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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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.*), BiobaseXNA (==0.9.3.*), 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.*), 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.*), 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

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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/