Information Theoretic Approaches to Whole Genome Phylogenies

摘要

We describe a novel method for efficient reconstruction of phylogenetic trees, based on sequences of whole genomes or proteomes. The core of our method is a new measure of pairwise distances between sequences, whose lengths may greatly vary. This measure is based on information theoretic tools (Kullback-Leibler relative entropy). We present an algorithm for efficiently computing these distances. The algorithm uses suffix arrays to compute the distance of two ￡ long sequences in 0 time. It is fast enough to enable the construction of the phylogenomic tree for hundreds of species, and the phylogenomic forest for almost two thousand viruses. An initial analysis of the results exhibits a remarkable agreement with "acceptable phylogenetic truth". To assess our approach, it was implemented together with a number of alternative approaches, including two that were previously published in the literature. Comparing their outcome to ours, using a "traditional" tree and a standard tree comparison method, ouralgorithm improved upon the "competition" by a substantial margin.