Figure 9

Underestimate of ML branch lengths for 8-taxon trees. Percentage that branch lengths were underestimated for datasets simulated on 8-taxon trees with equal branch lengths using the HKY model with a transition/transversion ratio of 2 and equal base frequencies, and analyzed using maximum likelihood with parameters estimated from the data. Depth 1 and depth 2 branches were graphed separately (white and gray boxes respectively. This analysis is equivalent to that of Figure 3, but conducted using an ML framework; refer to the Figure 3 inset for the simulation topology. (a) 1 kb datasets; (b) 10 kb datasets. Outliers (not shown) for depth 2 branches of 1.2 substitutions/site for 1 kb datasets were up to 30,000% overestimated (negatively underestimated) and were up to 50,000% overestimated for branch lengths of 1.4 substitutions/site.