Forestry: Comparison of trees and forests.

[ bioinformatics, bsd3, formal-languages, library ] [ Propose Tags ]

Wikipedia on forestry: "the science and craft of creating, managing, using, conserving, and repairing forests and associated resources."

This is a modest starting point and provides just:

  • forest alignments

  • tree alignments

Build this library and executable with GHC-8.0.2

To enable RNAforestry, use cabal new-build -frnaforestry or cabal new-configure -w compiler-path -frnaforestry && cabal new-build. We suggest using cabal with the nix-style local build options.


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Flags

Manual Flags

NameDescriptionDefault
rnaforestry

build the RNAforestry example application

Disabled

Use -f <flag> to enable a flag, or -f -<flag> to disable that flag. More info

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Versions [RSS] 0.0.0.1
Change log changelog.md
Dependencies ADPfusion (>=0.5.2 && <0.5.3), ADPfusionForest (>=0.0.0 && <0.0.1), base (>=4.7 && <5.0), BiobaseNewick (>=0.0.0 && <0.0.1), BiobaseTypes (>=0.1.3 && <0.1.4), containers, ForestStructures (>=0.0.0 && <0.0.1), FormalGrammars (>=0.3.1 && <0.3.2), lens (>=4.0), log-domain (>=0.11), PrimitiveArray (>=0.8.0 && <0.8.1), PrimitiveArray-Pretty (>=0.0.0 && <0.0.1), text (>=1.0), vector (>=0.10) [details]
License BSD-3-Clause
Copyright Christian Hoener zu Siederdissen, 2017
Author Christian Hoener zu Siederdissen, Sarah Berkemer, 2017
Maintainer choener@bioinf.uni-leipzig.de
Category Formal Languages, Bioinformatics
Home page https://github.com/choener/Forestry
Bug tracker https://github.com/choener/Forestry/issues
Source repo head: git clone git://github.com/choener/Forestry
Uploaded by ChristianHoener at 2017-11-23T22:47:08Z
Distributions NixOS:0.0.0.1
Executables RNAforestry
Downloads 954 total (5 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 2017-11-23 [all 1 reports]

Readme for Forestry-0.0.0.1

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Build Status

Forestry: Science and craft of forests

This library provides linear and affine tree alignment algorithms. In addition, a very simple program @RNAforestry@ is provided. This program mimics @RNAforester@.

Contact

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