On the repeat-annotated phylogenetic tree reconstruction problem

Firas Swidan, Michal Ziv-Ukelson, Ron Y. Pinter

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


A new problem in phylogenetic inference is presented, based on recent biological findings indicating a strong association between reversals (i.e., 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).

Original languageEnglish
Pages (from-to)1397-1418
Number of pages22
JournalJournal of Computational Biology
Issue number8
StatePublished - 1 Oct 2006
Externally publishedYes


  • Genome rearrangements
  • Phylogenetic inference
  • Repmaps
  • Set-tries

ASJC Scopus subject areas

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics


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