AlignmentAlgorithms: Collection of alignment algorithms

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

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.

https://github.com/choener/AlignmentAlgorithms/blob/master/README.md

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

Christian Hoener zu Siederdissen
Sneaking Around ConcatMap: Efficient Combinators for Dynamic Programming
2012. Proceedings of the 17th ACM SIGPLAN international conference on Functional programming
http://doi.acm.org/10.1145/2364527.2364559 preprint: http://www.tbi.univie.ac.at/newpapers/pdfs/TBI-p-2012-2.pdf
Andrew Farmer, Christian Höner zu Siederdissen, and Andy Gill.
The HERMIT in the stream: fusing stream fusion’s concatMap.
2014. Proceedings of the ACM SIGPLAN 2014 workshop on Partial evaluation and program manipulation.
http://dl.acm.org/citation.cfm?doid=2543728.2543736
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.
http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6819790
Christian Höner zu Siederdissen, Sonja J. Prohaska, and Peter F. Stadler.
Algebraic Dynamic Programming over General Data Structures.
2015. submitted.

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Versions [RSS] [faq] 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 (==0.4.0.*), base (>=4.7 && <4.9), containers (==0.5.*), fmlist (==0.9.*), FormalGrammars (==0.2.0.*), GrammarProducts (==0.1.0.*), PrimitiveArray (==0.6.0.*), vector (==0.10.*) [details]
License GPL-3.0-only
Copyright Christian Hoener zu Siederdissen, 2013-2015
Author Christian Hoener zu Siederdissen, 2013-2015
Maintainer choener@bioinf.uni-leipzig.de
Revised Revision 1 made by ChristianHoener at 2015-05-08T00:21:51Z
Category Algorithms, Data Structures, Bioinformatics, Linguistics
Home page http://www.bioinf.uni-leipzig.de/Software/gADP/
Source repo head: git clone git://github.com/choener/AlignmentAlgorithms
Uploaded by ChristianHoener at 2015-05-08T00:19:29Z
Distributions NixOS:0.1.0.0
Downloads 4047 total (35 in the last 30 days)
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Status Hackage Matrix CI
Docs available [build log]
Last success reported on 2015-10-01 [all 2 reports]

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Readme for AlignmentAlgorithms-0.0.1.0

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AlignmentAlgorithms

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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 choener@bioinf.uni-leipzig.de Leipzig University, Leipzig, Germany