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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Dependenciesaeson (>=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]
CopyrightChristian Hoener zu Siederdissen, 2011 - 2017
AuthorChristian Hoener zu Siederdissen
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Source repositoryhead: git clone git://
UploadedTue Mar 14 13:57:16 UTC 2017 by ChristianHoener



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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