AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics

TLDR

In Bayesian phylogenetics, successful MCMC inference depends on chain performance, yet convergence diagnostics are rarely used, and graphical exploration of MCMC output can reveal crucial information about analysis success. The authors present a simple tool that visualizes key properties of MCMC output, such as convergence rates of posterior split probabilities and branch lengths, to aid Bayesian phylogenetic analysis. The tool complements existing diagnostics, highlights that single‑parameter trace‑plots can be misleading, and is distributed as GPL‑licensed source and a web application. The study finds that relying on single‑parameter trace‑plots, such as likelihood scores, can mislead assessment of phylogenetic MCMC convergence.

Abstract

A key element to a successful Markov chain Monte Carlo (MCMC) inference is the programming and run performance of the Markov chain. However, the explicit use of quality assessments of the MCMC simulations-convergence diagnostics-in phylogenetics is still uncommon. Here, we present a simple tool that uses the output from MCMC simulations and visualizes a number of properties of primary interest in a Bayesian phylogenetic analysis, such as convergence rates of posterior split probabilities and branch lengths. Graphical exploration of the output from phylogenetic MCMC simulations gives intuitive and often crucial information on the success and reliability of the analysis. The tool presented here complements convergence diagnostics already available in other software packages primarily designed for other applications of MCMC. Importantly, the common practice of using trace-plots of a single parameter or summary statistic, such as the likelihood score of sampled trees, can be misleading for assessing the success of a phylogenetic MCMC simulation.The program is available as source under the GNU General Public License and as a web application at http://ceb.scs.fsu.edu/awty.