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Updated: Jul 9, 2026

A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
Topology-Bayes versus Clade-Bayes in phylogenetic analysis
Ward C Wheeler1, Kurt M Pickett
1Division of Invertebrate Zoology, American Museum of Natural History, NY, USA. wheeler@amnh.org
Abstract:
Several features of currently used Bayesian methods in phylogenetic analysis are discussed. The distinction between Clade-Bayes and Topology-Bayes is presented and illustrated with an empirical example. Three problems with Bayesian phylogenetic methods--exaggerated clade support, inconsistently biased priors, and the impossibility of hypothesis testing of cladograms--are shown to be the result of using a Clade-based Bayesian approach. Topology-based Bayesian methods do not share these shortcomings.
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