Note that this visualization is from v1.0 pplacer. We strongly suggest using the latest version; the corresponding visualizations can be seen on the new site.
We've worked to make useful visualizations for use with pplacer. Below is a visualization made with the pplacer program placeviz then viewed with the archaeopteryx Java applet (if it's not showing then Java isn't properly installed on your browser). The width of the edges is a linear function of the number of placements on that edge, and the color shows the average uncertainty of those placements according to expected distance between them.