title: Applying a multiobjective metaheuristic inspired by honey bees to phylogenetic inference.
abstract: The development of increasingly popular multiobjective metaheuristics has allowed bioinformaticians to deal with optimization problems in computational biology where multiple objective functions must be taken into account. One of the most relevant research topics that can benefit from these techniques is phylogenetic inference. Throughout the years, different researchers have proposed their own view about the reconstruction of ancestral evolutionary relationships among species. As a result, biologists often report different phylogenetic trees from a same dataset when considering distinct optimality principles. In this work, we detail a multiobjective swarm intelligence approach based on the novel Artificial Bee Colony algorithm for inferring phylogenies. The aim of this paper is to propose a complementary view of phylogenetics according to the maximum parsimony and maximum likelihood criteria, in order to generate a set of phylogenetic trees that represent a compromise between these principles. Experimental results on a variety of nucleotide data sets and statistical studies highlight the relevance of the proposal with regard to other multiobjective algorithms and state-of-the-art biological methods.
authors.affiliation: Department of Computer and Communications Technologies, University of Extremadura, Escuela Politécnica, Campus Universitario s/n, Caceres 10003, Spain. sesaji@unex.es
authors.forename: Sergio
authors.initials: S
authors.lastname: Santander-Jiménez
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Vega-Rodríguez
mesh_terms: D000465:Algorithms; D002965:Classification / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D016013:Likelihood Functions; D010802:Phylogeny
keywords: Bioinspired computation; Computational biology; Multiobjective optimization; Phylogeny reconstruction; Swarm intelligence