The BiobaseInfernal package

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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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Versions0.0.2.0, 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 logchangelog.md
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]
LicenseGPL-3
CopyrightChristian Hoener zu Siederdissen, 2011 - 2017
AuthorChristian Hoener zu Siederdissen
Maintainerchoener@bioinf.uni-leipzig.de
CategoryBioinformatics
Home pagehttps://github.com/choener/BiobaseInfernal
Bug trackerhttps://github.com/choener/BiobaseInfernal/issues
Source repositoryhead: git clone git://github.com/choener/BiobaseInfernal
ExecutablescmsearchFilter
UploadedTue Mar 14 13:57:16 UTC 2017 by ChristianHoener

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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/