title: Towards optimal distance functions for stochastic substitution models.
abstract: Distance based reconstruction methods of phylogenetic trees consist of two independent parts: first, inter-species distances are inferred assuming some stochastic model of sequence evolution; then the inferred distances are used to construct a tree. In this paper we concentrate on the task of inter-species distance estimation. Specifically, we characterize the family of valid distance functions for the assumed substitution model and show that deliberate selection of distance function significantly improves the accuracy of distance estimates and, consequently, also improves the accuracy of the reconstructed tree. Our contribution consists of three parts: first, we present a general framework for constructing families of additive distance functions for stochastic evolutionary models. Then, we present a method for selecting (near) optimal distance functions, and we conclude by presenting simulation results which support our theoretical analysis.
authors.affiliation: Technion, Computer Science, Taub Building, Technion City, 32000 Haifa, Israel. ilangr@cs.technion.ac.il
authors.forename: Ilan
authors.initials: I
authors.lastname: Gronau
authors.forename: Shlomo
authors.initials: S
authors.lastname: Moran
authors.forename: Irad
authors.initials: I
authors.lastname: Yavneh
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000235:genetics; D019143:Evolution, Molecular; D008390:Markov Chains; D008957:Models, Genetic; D010802:Phylogeny; D013269:Stochastic Processes
chemical_list: D004247:DNA