ADPfusionForest: Dynamic programming on tree and forest structures

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

ADPfusion for formal languages on tree and forest structures. This library connects @ForestStructures@, a library which defines efficient, tree-like structures and @ADPfusion@. The result is the ability to easily write formal grammars which act on input trees (as compared to the more common input strings).

Build this library with GHC-8.0.2

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Dependencies ADPfusion (==0.5.2.*), base (>=4.7 && <5.0), containers (>=0.5), DPutils (==0.0.1.*), fgl (>=5.5), ForestStructures (==0.0.0.*), GrammarProducts (==0.1.*), PrimitiveArray (==0.8.0.*), strict (>=0.3), text (>=1.2), unordered-containers (>=0.2), vector (>=0.10), vector-algorithms (>=0.7), vector-instances (>=3.4), vector-th-unbox (>=0.2) [details]
License BSD-3-Clause
Copyright Christian Hoener zu Siederdissen, 2016-2017
Author Christian Hoener zu Siederdissen, Sarah Berkemer, 2016-2017
Category Formal Languages, Bioinformatics
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Source repo head: git clone git://
Uploaded by ChristianHoener at 2017-11-23T22:15:26Z
Distributions NixOS:
Executables AffineAlignNewickTreesSmall, AlignNewickTrees
Downloads 928 total (12 in the last 30 days)
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Status Hackage Matrix CI
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Last success reported on 2017-11-24 [all 3 reports]


  • ADP
    • Fusion
      • Core
        • ForestAlign
          • ADP.Fusion.Core.ForestAlign.PermuteRightLinear
          • ADP.Fusion.Core.ForestAlign.RightLinear
        • ForestEdit
          • ADP.Fusion.Core.ForestEdit.LeftLinear
      • Forest
        • Align
          • ADP.Fusion.Forest.Align.PRL
          • ADP.Fusion.Forest.Align.RL
        • Edit
          • ADP.Fusion.Forest.Edit.LL
      • SynVar
        • Indices
          • ForestAlign
            • ADP.Fusion.SynVar.Indices.ForestAlign.RightLinear
          • ForestEdit
            • ADP.Fusion.SynVar.Indices.ForestEdit.LeftLinear
      • Term
        • Deletion
          • ForestAlign
            • ADP.Fusion.Term.Deletion.ForestAlign.RightLinear
          • ForestEdit
            • ADP.Fusion.Term.Deletion.ForestEdit.LeftLinear
        • Epsilon
          • ForestAlign
            • ADP.Fusion.Term.Epsilon.ForestAlign.PermuteRightLinear
            • ADP.Fusion.Term.Epsilon.ForestAlign.RightLinear
          • ForestEdit
            • ADP.Fusion.Term.Epsilon.ForestEdit.LeftLinear
        • Node
          • ForestAlign
            • ADP.Fusion.Term.Node.ForestAlign.PermuteRightLinear
            • ADP.Fusion.Term.Node.ForestAlign.RightLinear
          • ForestEdit
            • ADP.Fusion.Term.Node.ForestEdit.LeftLinear
          • ADP.Fusion.Term.Node.Type

Manual Flags


build the examples

Automatic Flags

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


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Readme for ADPfusionForest-

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ADPfusionForest: Dynamic and static tree and forest structures

This library extents ADPfusion to accept input in the form of trees and forests.

WARNING: Building with examples will leading to somewhat long compilation times.


Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany