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BiobaseNewick: Newick file format parser.
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 [RSS] | 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 && <0.0.2), QuickCheck (>=2.7), text (>=1.2), text-binary (>=0.1.0), vector (>=0.10) [details] |
| Tested with | ghc ==7.10.3, ghc ==8.0.1, ghc ==8.0.2 |
| License | BSD-3-Clause |
| Copyright | Christian Hoener zu Siederdissen, 2015-2017 |
| Author | Christian Hoener zu Siederdissen |
| Maintainer | choener@bioinf.uni-leipzig.de |
| Uploaded | by ChristianHoener at 2017-07-07T17:56:54Z |
| Revised | Revision 1 made by Bodigrim at 2023-08-02T22:22:20Z |
| Category | Bioinformatics |
| Home page | https://github.com/choener/BiobaseNewick |
| Bug tracker | https://github.com/choener/BiobaseNewick/issues |
| Source repo | head: git clone git://github.com/choener/BiobaseNewick |
| Distributions | LTSHaskell:0.0.0.2, NixOS:0.0.0.2, Stackage:0.0.0.2 |
| Reverse Dependencies | 2 direct, 2 indirect [details] |
| Executables | TestForestStructure |
| Downloads | 2339 total (8 in the last 30 days) |
| Rating | (no votes yet) [estimated by Bayesian average] |
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| Status | Docs available [build log] Last success reported on 2017-07-07 [all 1 reports] |
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 https://hackage.haskell.org/package/phybin which you might want instead.
Contact
Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany
choener@bioinf.uni-leipzig.de
https://www.bioinf.uni-leipzig.de/~choener/