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.

Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny / Urbini, L.; Sinaimeri, Blerina; Matias, C.; Sagot, M. -F.. - In: IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. - ISSN 1545-5963. - 16:3(2019), pp. 738-748. [10.1109/TCBB.2018.2838667]

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

Sinaimeri B.;
2019

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.
Cophylogeny; event-based methods; measure for tree reconciliation comparison; parsimony; robustness
Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny / Urbini, L.; Sinaimeri, Blerina; Matias, C.; Sagot, M. -F.. - In: IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. - ISSN 1545-5963. - 16:3(2019), pp. 738-748. [10.1109/TCBB.2018.2838667]
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11385/202495
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