Fig. 2.

Accuracy of branch length estimates in the simulated data set. For each method, model branch lengths b _e (x-axis) are plotted against estimation errors ${\widehat{b}}_e-b_e$ (y-axis) for all branches in all 500 model trees (500×77=38,500 points per plot). Colors (from blue to red) indicate increased density of points. The horizontal red line corresponds to no estimation error. Method names are shown at the top of each plot, followed by the mean (over 500 values) of the fraction of variance unexplained of (b _e) relative to $\left({\widehat{b}}_e\right)$ (see Additional file 3)