Estimating the Effective Sample Size of Tree Topologies from Bayesian Phylogenetic Analyses.

ABSTRACT: Bayesian phylogenetic analyses estimate posterior distributions of phylogenetic tree topologies and other parameters using Markov chain Monte Carlo (MCMC) methods. Before making inferences from these distributions, it is important to assess their adequacy. To this end, the effective sample size (ESS) estimates how many truly independent samples of a given parameter the output of the MCMC represents. The ESS of a parameter is frequently much lower than the number of samples taken from the MCMC because sequential samples from the chain can be non-independent due to autocorrelation. Typically, phylogeneticists use a rule of thumb that the ESS of all parameters should be greater than 200. However, we have no method to calculate an ESS of tree topology samples, despite the fact that the tree to

SUBMITTER: Lanfear R 

PROVIDER: S-EPMC5010905 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature