The BiobaseNewick package

[ Tags: bioinformatics, bsd3, library, program ] [ Propose Tags ]

This is a simple parser for Newick trees. The parser returns a rose tree. Each node is labelled with the node name (or an empty string for anonymous nodes) and a distance (0 if not given).

Includes conversion to an efficient static forest.


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Versions 0.0.0.1, 0.0.0.2
Change log changelog.md
Dependencies aeson (>=0.8), attoparsec (>=0.12), base (>=4.7 && <5.0), binary (>=0.7), BiobaseNewick, cereal (>=0.4), cereal-text (>=0.1.0), cmdargs (>=0.10), containers (>=0.5), fgl (>=5.5), ForestStructures (==0.0.0.*), QuickCheck (>=2.7), text (>=1.2), text-binary (>=0.1.0), vector (>=0.10) [details]
License BSD3
Copyright Christian Hoener zu Siederdissen, 2015-2017
Author Christian Hoener zu Siederdissen
Maintainer choener@bioinf.uni-leipzig.de
Category Bioinformatics
Home page https://github.com/choener/BiobaseNewick
Bug tracker https://github.com/choener/BiobaseNewick/issues
Source repository head: git clone git://github.com/choener/BiobaseNewick
Uploaded Fri Jul 7 17:56:54 UTC 2017 by ChristianHoener
Distributions LTSHaskell:0.0.0.2, NixOS:0.0.0.2, Stackage:0.0.0.2
Executables TestForestStructure
Downloads 160 total (7 in the last 30 days)
Rating 0.0 (0 ratings) [clear rating]
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Status Docs available [build log]
Last success reported on 2017-07-07 [all 1 reports]
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Readme for BiobaseNewick-0.0.0.2

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BiobaseNewick

This is a simple parser for Newick trees. The parser returns a rose tree. Each node is labelled with the node name (or an empty string for anonymous nodes) and a distance (0 if not given).

Newick trees can be ex- and imported into the Newick tree format. We also have serialization to the usual serializers.

This package was written mostly to complement a course a Univ. Leipzig. There is a more comprehensive package written by R. Newton http://hackage.haskell.org/package/phybin which you might want instead.

Contact

Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany
choener@bioinf.uni-leipzig.de
http://www.bioinf.uni-leipzig.de/~choener/