Preserving Inversion Phylogeny Reconstruction

  • Matthias Bernt
  • Kun-Mao Chao
  • Jyun-Wei Kao
  • Martin Middendorf
  • Eric Tannier
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7534)


Tractability results are rare in the comparison of gene orders for more than two genomes. Here we present a linear-time algorithm for the small parsimony problem (inferring ancestral genomes given a phylogeny on an arbitrary number of genomes) in the case gene orders are permutations, that evolve by inversions not breaking common gene intervals, and these intervals are organised in a linear structure. We present two examples where this allows to reconstruct the ancestral gene orders in phylogenies of several γ-Proteobacteria species and Burkholderia strains, respectively. We prove in addition that the large parsimony problem (where the phylogeny is output) remains NP-complete.


Character State Gene Order Binary Character Common Interval Signed Permutation 
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© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Matthias Bernt
    • 1
  • Kun-Mao Chao
    • 2
  • Jyun-Wei Kao
    • 2
  • Martin Middendorf
    • 1
  • Eric Tannier
    • 3
  1. 1.Parallel Computing and Complex Systems Group, Institute of Computer ScienceUniversity LeipzigGermany
  2. 2.Department of Computer Science and Information EngineeringNational Taiwan UniversityTaiwan
  3. 3.INRIA Rhône-Alpes; UMR CNRS 5558 “Biométrie et Biologie Évolutive”Université de Lyon 1VilleurbanneFrance

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