Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny

Laura Urbini 1, 2 Blerina Sinaimeri 1, 2 Catherine Matias 3 Marie-France Sagot 1, 2
1 ERABLE - Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale
Inria Grenoble - Rhône-Alpes
2 LBBE - Laboratoire de Biométrie et Biologie Evolutive
3 LPSM UMR 8001 - Laboratoire de Probabilités, Statistique et Modélisation
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 the tree reconciliation model is currently unable 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 : measure for tree reconciliation comparison cophylogeny parsimony event-based methods robustness
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Article dans une revue
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2018, pp.1-11. 〈10.1109/TCBB.2018.2838667〉
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Laura Urbini, Blerina Sinaimeri, Catherine Matias, Marie-France Sagot. Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2018, pp.1-11. 〈10.1109/TCBB.2018.2838667〉. 〈hal-01842451〉

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