An Alignment-Free Distance Measure for Closely Related Genomes

Authors:
Bernhard Haubold;Mirjana Domazet-Loso;Thomas Wiehe
Affiliations:
Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany;Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany and Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia;Institute of Genetics, Universität zu Köln, Cologne, Germany
Venue:
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Year:
2008

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Abstract

Phylogeny reconstruction on a genome scale remains computationally challenging even for closely related organisms. Here we propose an alignment-free pairwise distance measure, Kr, for genomes separated by less than approximately 0.5 mismatches/nucleotide. We have implemented the computation of Krbased on enhanced suffix arrays in the program kr, which is freely available from guanine.evolbio.mpg.de/kr/. The software is applied to genomes obtained from three sets of taxa: 27 primate mitochondria, eight Staphylococcus agalactiaestrains, and 12 Drosophilaspecies. Subsequent clustering of the Krvalues always recovers phylogenies that are similar or identical to the accepted branching order.