On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem

  • Firas Swidan
  • Michal Ziv-Ukelson
  • Ron Y. Pinter
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4009)


A new problem in phylogenetic inference is presented, based on recent biological findings indicating a strong association between reversals (aka inversions) and repeats. These biological findings are formalized here in a new mathematical model, called repeat-annotated phylogenetic trees (RAPT). We show that, under RAPT, the evolutionary process — including both the tree-topology as well as internal node genome orders — is uniquely determined, a property that is of major significance both in theory and in practice. Furthermore, the repeats are employed to provide linear-time algorithms for reconstructing both the genomic orders and the phylogeny, which are NP-hard problems under the classical model of sorting by reversals (SBR).


Edge Label Xanthomonas Campestris Repeat Pair Repeat Subsequence Legal Reversal 
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 2006

Authors and Affiliations

  • Firas Swidan
    • 1
    • 2
  • Michal Ziv-Ukelson
    • 1
    • 3
  • Ron Y. Pinter
    • 1
  1. 1.Department of Computer ScienceTechnion – Israel Institute of TechnologyHaifaIsrael
  2. 2.Janelia Farm, Howard Hughes Medical InstituteUSA
  3. 3.School of Computer ScienceTel-Aviv UniversityTel-AvivIsrael

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