Parallel multiple sequence alignment with local phylogeny search by simulated annealing

Authors:
Jaroslaw Zola;Denis Trystram;Andrei Tchernykh;Carlos Brizuela
Affiliations:
Laboratoire ID, IMAG, Montbonnot, France;Laboratoire ID, IMAG, Montbonnot, France;Computer Science Department, Ensenada, BC, Mexico;Computer Science Department, Ensenada, BC, Mexico
Venue:
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Year:
2006

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Abstract

The problem of multiple sequence alignment is one of the most important problems in computational biology. In this paper we present a new method that simultaneously performs multiple sequence alignment and phylogenetic tree inference for large input data sets. We describe a parallel implementation of our method that utilises simulated annealing metaheuristic to find locally optimal phylogenetic trees in reasonable time. To validate the method, we perform a set of experiments with synthetic as well as real-life data.