Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model.

ABSTRACT: Relaxed clock models enable estimation of molecular substitution rates across lineages and are widely used in phylogenetics for dating evolutionary divergence times. Under the (uncorrelated) relaxed clock model, tree branches are associated with molecular substitution rates which are independently and identically distributed. In this article we delved into the internal complexities of the relaxed clock model in order to develop efficient MCMC operators for Bayesian phylogenetic inference. We compared three substitution rate parameterisations, introduced an adaptive operator which learns the weights of other operators during MCMC, and we explored how relaxed clock model estimation can benefit from two cutting-edge proposal kernels: the AVMVN and Bactrian kernels. This work has produced an o

SUBMITTER: Douglas J 

PROVIDER: S-EPMC7880504 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature