On the importance of assessing topological convergence in Bayesian phylogenetic inference.

ABSTRACT: Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distribution. These algorithms require careful evaluation of the quality of the generated samples. Within the field of phylogenetics, one frequently adopted diagnostic approach is to evaluate the effective sample size (ESS) and to investigate trace graphs of the sampled parameters. A major limitation of these approaches is that they are developed for continuous parameters and therefore incompatible with a crucial parameter in these inferences: the tree topology. Several recent advancements have aimed at extending these diagnostics to topological space. In this reflection paper, we present two case studies

SUBMITTER: Brusselmans M 

PROVIDER: S-EPMC11383445 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature