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Bioinformatics Advance Access originally published online on August 30, 2007
Bioinformatics 2008 24(4):581-583; doi:10.1093/bioinformatics/btm388
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Johan A.A. Nylander 1, James C. Wilgenbusch 1,*, Dan L. Warren 2 and David L. Swofford 1

1School of Computational Sciences, Florida State University, Tallahassee, Florida 32306 and 2Section of Evolution and Ecology, University of California, Davis, California 95616, USA

*To whom correspondence should be addressed.


  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.

Availability: The program is available as source under the GNU General Public License and as a web application at http://ceb.scs.fsu.edu/awty

Contact: jwilgenb{at}scs.fsu.edu

Associate Editor: Keith Crandall

Received on February 8, 2007; revised on May 25, 2007; accepted on July 20, 2007

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