BiobaseInfernal: Infernal data structures and tools

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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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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
Category Bioinformatics
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Source repo head: git clone git://
Uploaded by ChristianHoener at 2017-03-14T13:57:16Z



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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.


Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany