This tutorial describes how to annotate an MCC tree with location states as inferred using a discrete phylogeographic inference. The tutorial build on the results from Discrete Phylogeographic Analysis and assumes you are using TreeAnnotator v1.2 or higher. We will visualize the MCC tree in FigTree (v1.2.3), but it can also be converted to KML for visualization in Google Earth (see Google Earth visualization).
Run TreeAnnotator and specify an appropriate burn-in. For visualization purposes, it will be useful to set the "Posterior probability limit" to zero. Choose "Maximum Clade Credibility Tree" as target tree and select "Mean heights" as node heights. Select the file containing the tree distribution (with annotated states), specify an "Output file" and run TreeAnnotator.
Open the resulting MCC tree in FigTree. In "Appearance", set the colour by "state". Turn on "Node labels" and set those to the modal state probability "state.prob". The complete state set for the nodes and their posterior probability can also be selected. In the figure below, red represents Guangdong, which appears to be the main location from which many other locations are seeded throughout the H5N1 epidemic history.