An Evolutionary Distance Based on Maximal Unique Matches

We propose to compare complete genomes using a new evolutionary distance based on maximum unique matches (MUMs). We first evaluate the minimum length for a MUM to be significant, and significant MUMs shared by two genomes are then searched with a linear time algorithm. Then, by simulating sets of sequences evolving according to a given tree topology, we prove that this distance varies monotonically with the amount of evolutionary events and, using the NJ method, we get phylogenetic trees very close to the initial ones. Finally, we apply this very fast method to compare bacterial genomes among the Gammaproteobacteria family.

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