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Science 21 April 2006:
Vol. 312. no. 5772, p. 367
DOI: 10.1126/science.1124180
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Technical Comments

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

Elchanan Mossel1* and Eric Vigoda2*

We presented a tree mixture in which Markov chain Monte Carlo (MCMC) methods have an exponentially slow convergence rate. We expect that many other mixture scenarios will show slow convergence. Ronquist et al. show that Metropolis-coupled MCMC (MC3) converges quickly on our mixture. However, they presented no theoretical or systematic experimental evidence determining the type of mixtures where MC3 or other methods are efficient.

1 Department of Statistics, University of California at Berkeley, Berkeley, CA 94720, USA.
2 College of Computing, Georgia Institute of Technology, Atlanta, GA 30332, USA.

* To whom correspondence should be addressed. E-mail: mossel{at}stat.berkeley.edu; E-mail: vigoda{at}cc.gatech.edu

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Science. ISSN 0036-8075 (print), 1095-9203 (online)