Figure 1.

Example application, showing uncertainty. Pplacer example application using psbA reference sequences and the corresponding recruited Global Ocean Sampling [4] (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 [32].

Matsen et al. BMC Bioinformatics 2010 11:538   doi:10.1186/1471-2105-11-538
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