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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build the RNAforestry example application


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


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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
Category Formal Languages, Bioinformatics
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Source repo head: git clone git://
Uploaded by ChristianHoener at 2017-11-23T22:47:08Z
Reverse Dependencies 1 direct, 0 indirect [details]
Executables RNAforestry
Downloads 1034 total (7 in the last 30 days)
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Status Docs available [build log]
Last success reported on 2017-11-23 [all 1 reports]

Readme for Forestry-

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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@.


Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany