title: Comment on "Phylogenetic MCMC algorithms are misleading on mixtures of trees".
abstract: 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.
authors.affiliation: School of Computational Science, Florida State University, Tallahassee, FL 32306-4120, USA. ronquist@scs.fsu.edu
authors.forename: Fredrik
authors.initials: F
authors.lastname: Ronquist
authors.forename: Bret
authors.initials: B
authors.lastname: Larget
authors.forename: John P
authors.initials: JP
authors.lastname: Huelsenbeck
authors.forename: Joseph B
authors.initials: JB
authors.lastname: Kadane
authors.forename: Donald
authors.initials: D
authors.lastname: Simon
authors.forename: Paul
authors.initials: P
authors.lastname: van der Mark
mesh_terms: D000465:Algorithms; D008390:Markov Chains; D008433:Mathematics; D009010:Monte Carlo Method; D010802:Phylogeny