Comment on "Phylogenetic MCMC algorithms are misleading on mixtures of trees".
Mossel and Vigoda (Reports, 30 September 2005, p. 2207) show that nearest neighbor interchange transitions, commonly used in phylogenetic Markov chain Monte Carlo (MCMC) algorithms, perform poorly on mixtures of dissimilar trees. However, the conditions leading to their results are artificial. Standard MCMC convergence diagnostics would detect the problem in real data, and correction of the model misspecification would solve it.
Ronquist
Fredrik
F
School of Computational Science, Florida State University, Tallahassee, FL 32306-4120, USA. ronquist@scs.fsu.edu
Larget
Bret
B
Huelsenbeck
John P
JP
Kadane
Joseph B
JB
Simon
Donald
D
van der Mark
Paul
P
D000465:Algorithms; D008390:Markov Chains; D008433:Mathematics; D009010:Monte Carlo Method; D010802:Phylogeny