AlignmentAlgorithms: Collection of alignment algorithms

[ algorithms, bioinformatics, data-structures, gpl, library, linguistics ] [ Propose Tags ]

generalized Algebraic Dynamic Programming

A selection of (sequence) alignment algorithms. Both terminal, and syntactic variables, as well as the index type is not fixed here. This makes it possible to select the correct structure of the grammar here, but bind the required data type for alignment in user code.

That being said, these algorithms are mostly aimed towards sequence alignment problems.

List of grammars for sequences:

  • global alignment

  • linear scoring: Needleman-Wunsch style

  • affine scoring: Gotoh

  • semiglobal alignment

  • overhang alignment

List of grammar for trees:

  • global alignment

  • linear scoring

  • affine scoring

  • simplified affine scoring

  • global editing

  • linear scoring

We now provide tree alignment and editing algorithms as well. We do not depend on ADPfusionForest to achieve this because grammar rules are completely disconnected from the underlying ADPfusion machinery.


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Versions [RSS] 0.0.1.0, 0.0.1.2, 0.0.2.0, 0.0.2.1, 0.1.0.0
Change log changelog.md
Dependencies ADPfusion (>=0.5.2 && <0.5.3), base (>=4.7 && <5.0), containers (>=0.5), fmlist (>=0.9), FormalGrammars (>=0.3.1 && <0.3.2), GrammarProducts (>=0.1.1 && <0.1.2), PrimitiveArray (>=0.8.0 && <0.8.1), vector (>=0.10) [details]
License GPL-3.0-only
Copyright Christian Hoener zu Siederdissen, 2013-2017
Author Christian Hoener zu Siederdissen, 2013-2017
Maintainer choener@bioinf.uni-leipzig.de
Category Algorithms, Data Structures, Bioinformatics, Linguistics
Home page https://github.com/choener/AlignmentAlgorithms
Bug tracker https://github.com/choener/AlignmentAlgorithms/issues
Source repo head: git clone git://github.com/choener/AlignmentAlgorithms
Uploaded by ChristianHoener at 2017-03-14T14:41:48Z
Distributions NixOS:0.1.0.0
Downloads 4370 total (13 in the last 30 days)
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Status Docs available [build log]
Last success reported on 2017-03-14 [all 1 reports]

Readme for AlignmentAlgorithms-0.1.0.0

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AlignmentAlgorithms

generalized ADPfusion Homepage

A selection of (sequence) alignment algorithms. Both terminal, and syntactic variables, as well as the index type is not fixed here. This makes it possible to select the correct structure of the grammar here, but bind the required data type for alignment in user code.

Contact

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