On the repeat-annotated phylogenetic tree reconstruction problem

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

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Scopus citations


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 phyImjenetic 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 practico. 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
Title of host publicationCombinatorial Pattern Matching - 17th Annual Symposium, CPM 2006, Proceedings
PublisherSpringer Verlag
Number of pages12
ISBN (Print)3540354557, 9783540354550
StatePublished - 1 Jan 2006
Externally publishedYes
Event17th Annual Symposium on Combinatorial Pattern Matching, CPM 2006 - Barcelona, Spain
Duration: 5 Jul 20067 Jul 2006

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4009 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference17th Annual Symposium on Combinatorial Pattern Matching, CPM 2006

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science (all)


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