Technical Comments

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

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Science  21 Apr 2006:
Vol. 312, Issue 5772, pp. 367
DOI: 10.1126/science.1124180

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Abstract

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.

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