Abstract
We describe a Branch-and-Bound algorithm for computing a parsimonious species tree given a set of gene family trees. Our algorithm can compute a parsimonious species tree for 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.