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BiobaseInfernal: Infernal data structures and tools

[ bioinformatics, gpl, library, program ] [ Propose Tags ] [ Report a vulnerability ]

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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Modules

[Last Documentation]

  • 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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Versions [RSS] 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 && <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]
Tested with ghc ==7.10.3, ghc ==8.0.1
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 2017-03-14T13:57:23Z
Distributions
Reverse Dependencies 3 direct, 0 indirect [details]
Executables cmsearchFilter
Downloads 15994 total (17 in the last 30 days)
Rating (no votes yet) [estimated by Bayesian average]
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Status Docs not available [build log]
Last success reported on 2017-03-14 [all 2 reports]

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/