The GrammarProducts package

[Tags: gpl, library]

generalized Algebraic Dynamic Programming

An algebra of liner and context-free grammars.

This library provides the implementation of our theory of algebraic operations over linear and context-free grammars. Using algebraic operations, it is possible to construct complex dynamic programming algorithms from simpler atomic grammars.

Our most important contribution is the definition of a product of grammars which naturally leads to alignment-like algorithms on multiple tapes.

An efficient implementation of the resulting grammars is possible via the ADPfusion framework. The FormalGrammars library provides the required Template Haskell machinery. GramarProducts can be integrated as a plugin into the existing transformation from DSL to ADPfusion. Haskell users can just use the QQ function provided in the .QQ module.

Alternatively, the resulting grammars can also be pretty-printed in various ways (LaTeX, ANSI, Haskell module with signature and grammar).

The formal background can be found in two papers given in the README. The gADP homepage has further details, tutorials, examples.

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DependenciesADPfusion (==0.5.1.*), ansi-wl-pprint (==0.6.*), base (>=4.7 && <4.9), bytestring (==0.10.*), containers (==0.5.*), data-default (==0.5.*), FormalGrammars (>=0.2.1 && <0.3.1), lens (==4.*), newtype (==0.2.*), parsers (==0.12.*), PrimitiveArray (>= && <0.7.1), semigroups (>=0.15 && <0.19), template-haskell (==2.*), transformers (==0.4.*), trifecta (==1.5.*) [details]
CopyrightChristian Hoener zu Siederdissen, 2013-2016
AuthorChristian Hoener zu Siederdissen, 2013-2016
CategoryFormal Languages, Bioinformatics
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Source repositoryhead: git clone git://
UploadedMon Mar 14 00:36:40 UTC 2016 by ChristianHoener
Downloads971 total (16 in last 30 days)
0 []
StatusDocs available [build log]
Last success reported on 2016-03-14 [all 1 reports]




examplesbuild the examples (only Needleman-Wunsch for now)DisabledManual

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Readme for GrammarProducts-

GrammarProducts: Products of formal languages

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generalized Algebraic Dynamic Programming Homepage

An abstract algebra for linear and context-free grammars.

  1. Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler.
    Product Grammars for Alignment and Folding
    2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics. 99
  2. Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler.
    How to Multiply Dynamic Programming Algorithms
    2013, Brazilian Symposium on Bioinformatics (BSB 2013)
    Lecture Notes in Bioinformatics 8213. Springer, Heidelberg.
    paper preprint


Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany