The Taub Faculty of Computer Science Events and Talks

Distance based reconstruction methods of phylogenetic trees are split into two independent parts: first, inter-species distances are inferred using some stochastic model of sequence evolution; then the inferred distances are used to construct a tree. Most research in this area focuses on the second task. This talk concentrates on the task of inter-species distance estimation, and provides a general characterization of distance functions for stochastic substitution models. Then it will be shown that by a deliberate selection of the distance function used, it is possible to significantly improve the accuracy of distance estimates.

The talk 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 simulations which support our theoretical analysis. Joint work with Ilan Gronau and Irad Yavneh.