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.
['Jaroslaw Zola', 'Denis Trystram', 'Andrei Tchernykh', 'Carlos A. Brizuela']
Parallel multiple sequence alignment with local phylogeny search by simulated annealing