Accounting for Gene Tree Uncertainties Improves Gene Trees and Reconciliation Inference

  • Thi Hau Nguyen
  • Jean-Philippe Doyon
  • Stéphanie Pointet
  • Anne-Muriel Arigon Chifolleau
  • Vincent Ranwez
  • Vincent Berry
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7534)


We propose a reconciliation heuristic accounting for gene duplications, losses and horizontal transfers that specifically takes into account the uncertainties in the gene tree. Rearrangements are tried for gene tree edges that are weakly supported, and are accepted whenever they improve the reconciliation cost. We prove useful properties on the dynamic programming matrix used to compute reconciliations, which allows to speed-up the tree space exploration when rearrangements are generated by Nearest Neighbor Interchanges (NNI) edit operations. Experimental results on simulated and real data confirm that running times are greatly reduced when considering the above-mentioned optimization in comparison to the naïve rearrangement procedure. Results also show that gene trees modified by such NNI rearrangements are closer to the correct (simulated) trees and lead to more correct event predictions on average. The program is available at Mowgli/


Gene Tree Cost Matrix Weak Edge Dynamic Programming Matrix Near Neighbor Interchange 
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 2012

Authors and Affiliations

  • Thi Hau Nguyen
    • 1
    • 2
  • Jean-Philippe Doyon
    • 1
  • Stéphanie Pointet
    • 1
  • Anne-Muriel Arigon Chifolleau
    • 1
  • Vincent Ranwez
    • 2
  • Vincent Berry
    • 1
  1. 1.LIRMM, Université Montpellier 2 - CNRSFrance
  2. 2.Montpellier SupAgro (UMR AGAP)France

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