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

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.

给定一组基因家族树，我们描述了一种用于计算简约物种树的分支定界算法。我们的算法可以考虑三种成本度量：基因重复的数量、基因丢失的数量以及两者的结合。此外，为了应对分支定界算法在物种树推断中关于可考虑的分类群数量的内在局限性，我们的算法可以自然地考虑分类群集合之间的预定义关系。我们在一个涵盖29个分类群的真核基因家族数据集上对我们的算法进行了测试。