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International Conference on Algorithms for Computational Biology

AlCoB 2016: Algorithms for Computational Biology pp 119–130Cite as

Robustness of the Parsimonious Reconciliation Method in Cophylogeny

Part of the Lecture Notes in Computer Science book series (LNBI,volume 9702)

Abstract

The aim of this paper is to explore the robustness of the parsimonious host-symbiont tree reconciliation method under editing or small perturbations of the input. The editing involves making different choices of unique symbiont mapping to a host in the case where multiple associations exist. This is made necessary by the fact that no tree reconciliation method is currently able to handle such associations. The analysis performed could however also address the problem of errors. The perturbations are re-rootings of the symbiont tree to deal with a possibly wrong placement of the root specially in the case of fast-evolving species. In order to do this robustness analysis, we introduce a simulation scheme specifically designed for the host-symbiont cophylogeny context, as well as a measure to compare sets of tree reconciliations, both of which are of interest by themselves.

Keywords

  • Cophylogeny
  • Parsimony
  • Event-based methods
  • Robustness
  • Measure for tree reconciliation comparison

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Acknowledgments

The authors would like to express their gratitude to Christian Gautier for fruitful preliminary discussions on this work.

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Authors and Affiliations

  1. Université Lyon 1, Villeurbanne, France

    Laura Urbini, Blerina Sinaimeri & Marie-France Sagot

  2. CNRS, UMR5558, Laboratoire de Biométrie Et Biologie Évolutive, 69622, Villeurbanne, France

    Laura Urbini, Blerina Sinaimeri & Marie-France Sagot

  3. INRIA Grenoble Rhône - Alpes, Montbonnot-Saint-Martin, France

    Laura Urbini, Blerina Sinaimeri & Marie-France Sagot

  4. Sorbonne Universités, Université Pierre et Marie Curie, Université Paris Diderot, Centre National de la Recherche Scientifique, Laboratoire de Probabilités et Modèles Aléatoires, 4 Place Jussieu, Paris, France

    Catherine Matias

Authors
  1. Laura Urbini
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  2. Blerina Sinaimeri
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  3. Catherine Matias
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  4. Marie-France Sagot
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Corresponding author

Correspondence to Blerina Sinaimeri .

Editor information

Editors and Affiliations

  1. CETA-Ciemat , Trujillo, Spain

    María Botón-Fernández

  2. Rovira i Virgili University , Tarragona, Spain

    Carlos Martín-Vide

  3. University of Extremadura , Cáceres, Spain

    Sergio Santander-Jiménez

  4. University of Extremadura , Cáceres, Spain

    Miguel A. Vega-Rodríguez

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Urbini, L., Sinaimeri, B., Matias, C., Sagot, MF. (2016). Robustness of the Parsimonious Reconciliation Method in Cophylogeny. In: Botón-Fernández, M., Martín-Vide, C., Santander-Jiménez, S., Vega-Rodríguez, M. (eds) Algorithms for Computational Biology. AlCoB 2016. Lecture Notes in Computer Science(), vol 9702. Springer, Cham. https://doi.org/10.1007/978-3-319-38827-4_10

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  • DOI: https://doi.org/10.1007/978-3-319-38827-4_10

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