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AWTY (Are We There Yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics (2007)
| Citations: | 108 - 5 self |
BibTeX
@MISC{Nylander07awty(are,
author = {Johan A. A. Nylander and James C. Wilgenbusch and Dan L. Warren and David L. Swofford},
title = {AWTY (Are We There Yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics},
year = {2007}
}
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Abstract
Summary: 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.
Keyphrases
graphical exploration bayesian phylogenetics mcmc convergence phylogenetic mcmc simulation sampled tree single parameter convergence rate successful markov chain monte carlo mcmc simulation convergence diagnostics markov chain bayesian phylogenetic analysis software package explicit use key element summary statistic likelihood score crucial information primary interest quality assessment common practice branch length mcmc simulation simple tool posterior split probability
