Speeding up the Computation of the Marginal Possibility of a Tree Topology

19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology

We study methods to quickly compute the marginal likelihood of a single fixed tree topology.We benchmark the speedand accuracy of 19 different methods to compute the marginal likelihood of phylogenetic topologies on a suite of real datasets.These methods include several new ones that we develop explicitly to solve this problem, as well as existing algorithms that we apply to phylogenetic models for the first time.Our results show that the accuracy of these methods varies widely, and that accuracy does not necessarily correlate with computational burden.Our newly developed methods are orders of magnitude faster than standard approaches, and in some cases, their accuracy rivals the best establishedestimators.