The GrammarProducts package

[Tags: gpl, library, program]

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 machinary.

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

Formal background can be found in two papers:

Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler
Product Grammars for Alignment and Folding
submitted

and

Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler
How to Multiply Dynamic Programming Algorithms
Brazilian Symposium on Bioinformatics (BSB 2013)
Lecture Notes in Bioinformatics 8213, Springer, Heidelberg

Properties

Versions0.0.0.2, 0.0.0.3, 0.0.0.4
DependenciesADPfusion (>=0.2.0), ansi-wl-pprint, base (==4.*), bytestring, cmdargs (==0.10.*), containers, data-default, FormalGrammars (>=0.0.0.2), HaTeX, lens, newtype, parsers, PrimitiveArray (>=0.5.1.0), semigroups, transformers, trifecta
LicenseGPL-3
CopyrightChristian Hoener zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler, 2013
AuthorChristian Hoener zu Siederdissen, 2013
Maintainerchoener@tbi.univie.ac.at
Stabilityexperimental
CategoryFormal Languages, Bioinformatics
Home pagehttp://www.tbi.univie.ac.at/~choener/gramprod
Source repositoryhead: git clone git://github.com/choener/GrammarProducts
ExecutablesGrammarProductPP
Upload dateSun Dec 22 23:03:08 UTC 2013
Uploaded byChristianHoener
Downloads233 total (24 in last 30 days)

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