19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology
Skip to main content
Open Access Publications from the University of California

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

  • Author(s): Fourment, Mathieu
  • Magee, Andrew F
  • Whidden, Chris
  • Bilge, Arman
  • IV, Frederick A Matsen
  • Minin, Vladimir N
  • et al.
Creative Commons Attribution 4.0 International Public License

The marginal likelihood of a model is a key quantity for assessing the evidence provided by the data in support of a model. The marginal likelihood is the normalizing constant for the posterior density, obtained by integrating the product of the likelihood and the prior with respect to model parameters. Thus, the computational burden of computing the marginal likelihood scales with the dimension of the parameter space. In phylogenetics, where we work with tree topologies that are high-dimensional models, standard approaches to computing marginal likelihoods are very slow. Here we study methods to quickly compute the marginal likelihood of a single fixed tree topology. We benchmark the speed and 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. Altogether, 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 established estimators.

Many UC-authored scholarly publications are freely available on this site because of the UC Academic Senate's Open Access Policy. Let us know how this access is important for you.

Main Content
Current View