An Extended Clade Framework for Annotated Trees in the Context of Phylogeography and Transmission Tree Inference (opens in new tab)

Bayesian phylogenetic inference produces large samples from a posterior distribution over phylogenetic trees that represents uncertainty in both tree topology and associated variables. Such a collection of trees is hard to interpret and it is common practice to summarize such samples into a single representative tree. Methods for constructing representative trees have largely been restricted to plain tree topologies, encoding only relationships among taxa. Inference with more sophisticated mo...