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Branch-and-Bound Approach for Parsimonious Inference of a Species Tree from a Set of Gene Family Trees

Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 696)

Abstract

We describe a Branch-and-Bound algorithm for computing a parsimonious species tree, given a set of gene family trees. Our algorithm can consider three cost measures: number of gene duplications, number of gene losses, and both combined. Moreover, to cope with intrinsic limitations of Branch-and-Bound algorithms for species trees inference regarding the number of taxa that can be considered, our algorithm can naturally take into account predefined relationships between sets of taxa. We test our algorithm on a dataset of eukaryotic gene families spanning 29 taxa.

Keywords

Comparative genomics Evolution and phylogenetics 

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.LIRMM, Université Montpellier 2 and CNRSMontpellierFrance

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