Alignment Free String Distances for Phylogeny

Abstract

In this paper, we compare the accuracy of four string distances to recover correct phylogenies of complete genomes. These distances are based on common words shared by raw genomic sequences and do not require preliminary processing steps such as gene identification or sequence alignment. Moreover, they are computable in linear time. The first distance is based on Maximum Significant Matches. The second is computed from the frequencies of all the words of length k. The third one is based on the Average length of maximum Common Substrings at any position. The last one is based on the Ziv-Lempel compression algorithm. We describe a simulation process of evolution to generate a set of sequences having evolved according to a random tree topology T. This process allows both base substitutions and fragment insertion/deletion, including horizontal gene transfers. The distances between the generated sequences are computed using the four string formulas and the corresponding trees T′ are reconstructed using Neighbor-Joining. Trees T and T′ are compared using three topological criteria. These comparisons show that the MSM distance outperforms the others whatever the parameters used to generate sequences.