biostudies-literatureBaele GEuropean Research CouncilNCRR NIH HHSEuropean Commission FP7NHGRI NIH HHSNINDS NIH HHSWellcome TrustNIGMS NIH HHS2157-67https://www.ebi.ac.uk/biostudies/studies/S-EPMC3424409biostudies-literatureUnknown29(9)Recent developments in marginal likelihood estimation for model selection in the field of Bayesian phylogenetics and molecular evolution have emphasized the poor performance of the harmonic mean estimator (HME). Although these studies have shown the merits of new approaches applied to standard normally distributed examples and small real-world data sets, not much is currently known concerning the performance and computational issues of these methods when fitting complex evolutionary and population genetic models to empirical real-world data sets. Further, these approaches have not yet seen widespread application in the field due to the lack of implementations of these computationally demanding techniques in commonly used phylogenetic packages. We here investigate the performance of some ofMolecular biology and evolutionImproving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty.PMC3424409R01 GM086887WT092807MAR01 NS063897U54 RR024386-01A2FP7_260864R01 HG006139FP7_278433260864095831Rambaut AAlekseyenko AVBaele GSuchard MALemey PBedford TfalseImproving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty.Recent developments in marginal likelihood estimation for model selection in the field of Bayesian phylogenetics and molecular evolution have emphasized the poor performance of the harmonic mean estimator (HME). Although these studies have shown the merits of new approaches applied to standard normally distributed examples and small real-world data sets, not much is currently known concerning the performance and computational issues of these methods when fitting complex evolutionary and population genetic models to empirical real-world data sets. Further, these approaches have not yet seen widespread application in the field due to the lack of implementations of these computationally demanding techniques in commonly used phylogenetic packages. We here investigate the performance of some of2012-01-01T00:00:00Z2012 Sep2025-06-25T03:06:07.428Z2025-06-25T03:06:07.428ZS-EPMC34244092240323910.1093/molbev/mss084