Example application, showing uncertainty. Pplacer example application using psbA reference sequences and the corresponding recruited Global Ocean Sampling  (GOS) sequences showing both number of placements and their uncertainty. Branch thickness is a linear function of the log-transformed number of placements on that edge, and branch color represents average uncertainty (more red implies more uncertain, with yellow denoting EDPL above a user-defined limit). The upper panel shows the Prochlorococcus clade of the tree. The lower panel shows a portion of the tree with substantial uncertainty using the EDPL metric. Placeviz output viewed using Archaeopteryx .
Matsen et al. BMC Bioinformatics 2010 11:538 doi:10.1186/1471-2105-11-538