The BiobaseInfernal package

[ Tags: benchmark, bioinformatics, gpl, library, program ] [ Propose Tags ]

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
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
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 repository head: git clone git://github.com/choener/BiobaseInfernal
Uploaded Tue Mar 14 13:57:23 UTC 2017 by ChristianHoener
Distributions NixOS:0.8.1.0
Executables cmsearchFilter
Downloads 5708 total (515 in the last 30 days)
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Status Docs not available [build log]
Last success reported on 2017-03-14 [all 2 reports]
Hackage Matrix CI

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

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Maintainer's Corner

For package maintainers and hackage trustees


Readme for BiobaseInfernal-0.8.1.0

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Build Status

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/