Maximum parsimony phylogenetic inference using simulated annealing

Abstract

The Maximum Parsimony (MP) problem aims at reconstructing a phylogenetic tree from DNA sequences while minimizing the total number of genetic transformations. In this paper we propose a carefully devised simulated annealing implementation, called SAMPARS (Simulated Annealing for Maximum PARSimony), for finding near-optimal solutions for the MP problem. Different possibilities for its key components and input parameter values were carefully analyzed and tunned in order to find the combination of them offering the best quality solutions to the problem at a reasonable computational effort. Its performance is investigated through extensive experimentation over well known benchmark instances showing that our SAMPARS algorithm is able to improve some previous best-known solutions. © Springer-Verlag Berlin Heidelberg 2013.