Inferring phylogeny | Find tree with maximum posterior probability; evaluate features in common among the sampled trees | (1–3) |

Evaluating uncertainty in phylogenies | Evaluate 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 analyses | Perform analysis on many trees, and weight results by the probability that each tree is correct | (41–43) |

Divergence times | Use fossils as a calibration. Infer divergence times by using a strict or relaxed molecular clock | (44) |

Testing molecular clock | Calculate Bayes factor for the clock versus no branch length restrictions | (24) |