@hackage AlignmentAlgorithms0.0.1.2

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.

• global alignment (Needleman-Wunsch style)

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.