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Towards Optimal Distance Functions for Stochastic Substitutions Models

By Ilan Gronau, Shlomo Moran and Irad Yavneh


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 interspecies 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. 1 Introduction. One of the most popular approaches to phylogenetic reconstruction is the distance based approach. This approach associates lengths to the edges of the phylogenetic tree. The additive distance between tw

Year: 2009
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