Comment on "Phylogenetic MCMC Algorithms Are Misleading on Mixtures of Trees"

doi:10.1126/science.1123622

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Comment on "Phylogenetic MCMC Algorithms Are Misleading on Mixtures of Trees"

Fredrik Ronquist,¹^* Bret Larget,² John P. Huelsenbeck,³ Joseph B. Kadane,⁴ Donald Simon,⁵ Paul van der Mark¹

Mossel and Vigoda (Reports, 30 September 2005, p. 2207) showthat nearest neighbor interchange transitions, commonly usedin phylogenetic Markov chain Monte Carlo (MCMC) algorithms,perform poorly on mixtures of dissimilar trees. However, theconditions leading to their results are artificial. StandardMCMC convergence diagnostics would detect the problem in realdata, and correction of the model misspecification would solveit.

¹ School of Computational Science, Florida State University, Tallahassee, FL 32306–4120, USA.
² Department of Statistics, University of Wisconsin, Madison, WI 53706, USA.
³ Division of Biological Sciences, University of California at San Diego, San Diego, CA 92093–0116, USA.
⁴ Department of Statistics, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
⁵ Department of Mathematics and Computer Science, Duquesne University, Pittsburgh, PA 15282, USA.

^* To whom correspondence should be addressed. E-mail: ronquist{at}scs.fsu.edu

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TECHNICAL COMMENTS Response to Comment on "Phylogenetic MCMC Algorithms Are Misleading on Mixtures of Trees": Elchanan Mossel and Eric Vigoda (21 April 2006)
Science 312 (5772), 367b. [DOI: 10.1126/science.1124180]
| Abstract » | Full Text » | PDF »

REPORTS Phylogenetic MCMC Algorithms Are Misleading on Mixtures of Trees: Elchanan Mossel and Eric Vigoda (30 September 2005)
Science 309 (5744), 2207. [DOI: 10.1126/science.1115493]
| Abstract » | Full Text » | PDF » | Supporting Online Material »