Bootstrapping Algorithms for Gene Duplication and Speciation Events

摘要

Based on the classical non-parametric bootstrapping for phy-logenetic trees, we propose a novel bootstrap method to define support for gene duplication and speciation events. While this approach can be used to annotate orthology and paralogy, we show how it can be used to verify reliability of tree reconciliation with applications to the problem of rooting of an unrooted gene tree. We propose a linear time algorithm for the computation of bootstrap values and we show the correspondence of our method with the classical non-parametric bootstrapping. Finally, based on simulated data and nine yeast genomes we present a comparative study of tree rooting methods and evaluation of their performance by using our bootstrapping method. The software and examples are publicly available.