The Average Common Substring Approach to Phylogenomic Reconstruction

Igor Ulitsky, David Burstein, Tamir Tuller, Benny Chor
2006 Journal of Computational Biology  
We describe a novel method for efficient reconstruction of phylogenetic trees, based on sequences of whole genomes or proteomes, whose lengths may greatly vary. The core of our method is a new measure of pairwise distances between sequences. This measure is based on computing the average lengths of maximum common substrings. It is intrinsically related to information theoretic tools (Kullback-Leibler relative entropy). We present an algorithm for efficiently computing these distances. In
more » ... le, the distance of two long sequences can be calculated in O( ) time. We implemented the algorithm, using suffix arrays. The implementation is fast enough to enable the construction of the proteome phylogenomic tree for hundreds of species, and the genome phylogenomic forest for almost two thousand viruses. An initial analysis of the results exhibits a remarkable agreement with "acceptable phylogenetic and taxonomic truth". To assess our approach, it was compared to the traditional (single gene or protein based) maximum likelihood method. It was compared to implementations of a number of alternative approaches, including two that were previously published in the literature, and to the published results of a third approach. Comparing their outcome and running time to ours, using a "traditional" trees and a standard tree comparison method, our algorithm improved upon the "competition" by a substantial margin. The simplicity and speed of our method allows for a whole genome analysis with the greatest scope attempted so far. We describe here five different applications of the method, which not only show the validity of the method, but also suggest a number of novel phylogenetic insights.
doi:10.1089/cmb.2006.13.336 pmid:16597244 fatcat:l2y4ypheo5bbncforxo55ffqdi