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An Alignment-Free Distance Measure for Closely Related Genomes

  • Bernhard Haubold
  • Mirjana Domazet-Los̆o
  • Thomas Wiehe
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5267)

Abstract

Phylogeny reconstruction on a genome scale remains computationally challenging even for closely related organisms. Here we propose an alignment-free pairwise distance measure, K r, for genomes separated by less than approximately 0.5 mismatches/nucleotide. We have implemented the computation of K r based 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 agalactiae strains, and 12 Drosophila species. Subsequent clustering of the K r values always recovers phylogenies that are similar or identical to the accepted branching order.

Keywords

Drosophila Species Guide Tree Drosophila Genome Phylogeny Reconstruction Streptococcus Agalactiae 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Bernhard Haubold
    • 1
  • Mirjana Domazet-Los̆o
    • 1
    • 2
  • Thomas Wiehe
    • 3
  1. 1.Department of Evolutionary GeneticsMax-Planck-Institute for Evolutionary BiologyPlönGermany
  2. 2.Faculty of Electrical Engineering and ComputingUniversity of ZagrebZagrebCroatia
  3. 3.Institute of GeneticsUniversität zu KölnCologneGermany

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