An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework

@article{Doyon2012AnEM,
  title={An Efficient Method for Exploring the Space of Gene Tree/Species Tree Reconciliations in a Probabilistic Framework},
  author={Jean-Philippe Doyon and Sylvie Hamel and C{\'e}dric Chauve},
  journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  year={2012},
  volume={9},
  pages={26-39}
}
Background. Inferring an evolutionary scenario for a gene family is a fundamental problem with applications both in functional and evolutionary genomics. The gene tree/species tree reconciliation approach has been widely used to address this problem, but mostly in a discrete parsimony framework that aims at minimizing the number of gene duplications and/or gene losses. Recently, a probabilistic approach has been developed, based on the classical birth-and-death process, including efficient… 
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