Evolution of Genes Neighborhood within Reconciled Phylogenies: An Ensemble Approach

  • Cedric Chauve
  • Yann Ponty
  • João Paulo Pereira Zanetti
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8826)


We consider a recently introduced dynamic programming scheme to compute parsimonious evolutionary scenarios for gene adjacencies. We extend this scheme to sample evolutionary scenarios from the whole solution space under the Boltzmann distribution. We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic inconsistencies observed in the resulting ancestral gene adjacencies.


Partition Function Gene Neighborhood Boltzmann Distribution Ancestral Gene Ensemble Approach 
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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Cedric Chauve
    • 1
  • Yann Ponty
    • 1
    • 2
  • João Paulo Pereira Zanetti
    • 1
    • 3
    • 4
  1. 1.Department of MathematicsSimon Fraser UniversityBurnabyCanada
  2. 2.Pacific Institute for Mathematical Sciences, CNRS UMI3069VancouverCanada
  3. 3.Institute of Computing, UNICAMPCampinasBrazil
  4. 4.São Paulo Research Foundation, FAPESPSão PauloBrazil

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