LIRMM, Université Montpellier 2 and CNRS, Montpellier, France.
Adv Exp Med Biol. 2011;696:287-95. doi: 10.1007/978-1-4419-7046-6_29.
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.
我们描述了一种分支定界算法，用于计算给定一组基因家族树的简约物种树。我们的算法可以考虑三种代价度量：基因复制数、基因丢失数以及两者的组合。此外，为了解决物种树推断中分支定界算法对可考虑分类单元数量的固有限制，我们的算法可以自然地考虑分类单元集合之间预定义的关系。我们在一个包含 29 个分类单元的真核基因家族数据集上测试了我们的算法。
