Parallel multiple sequence alignment with local phylogeny search by simulated annealing

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