Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations

Authors:
Jean-Philippe Doyon;Cedric Chauve;Sylvie Hamel
Affiliations:
DIRO, Université de Montréal, Montréal (QC), Canada H3C 3J7;Department of Mathematics, Simon Fraser University, Canada V5A 1S6;DIRO, Université de Montréal, Montréal (QC), Canada H3C 3J7
Venue:
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Year:
2008

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Abstract

We describe algorithms to explore the space of all possible reconciliations between a gene tree and a species tree. We propose an algorithm for generating a random reconciliation, and combinatorial operators and algorithms to explore the space of all possible reconciliations between a gene tree and a species tree in optimal time. We apply these algorithms to simulated data.