Table 1. The Bayesian approach to problems in phylogeny.

ProblemBayesian approach Ref.
Inferring phylogenyFind tree with maximum posterior probability; evaluate features in common among the sampled trees(1–3)
Evaluating uncertainty in phylogeniesEvaluate clade probabilities; form credible set containing trees whose cumulative probability sums to 0.95(3, 40)
Detecting selection Model substitution process on the codon and calculate probability of being in purifying or positively selected class; sample substitutions and count number of synonymous and nonsynonymous changes(29,32)
Comparative analysesPerform analysis on many trees, and weight results by the probability that each tree is correct(41–43)
Divergence timesUse fossils as a calibration. Infer divergence times by using a strict or relaxed molecular clock(44)
Testing molecular clockCalculate Bayes factor for the clock versus no branch length restrictions(24)