On this page I do a quick survey of some of the tree priors available in BEAST and how they might influence estimation of dates (and therefore rates) when used in common ways.
For the illustrative purposes of this example I am going to use a small data set of Primates (Primates.nex) that is available with the distribution of BEAST.
For each tree prior we will do a Bayesian analysis and we will calibrate the divergence times of the tree by providing a uniform prior distribution (0.1-10) on the overall rate of evolution (parameter). In general I thoroughly dislike uniform priors as they are usually poor descriptors of our prior knowledge.
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