Figure 8

Underestimate of ML branch lengths for 4-taxon trees. Percentage that branch lengths were underestimated for 1 and 10 kb datasets simulated on 4-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. This analysis is equivalent to that of Figure 2, but conducted using an ML framework; refer to the Figure 2 inset for the simulation topology.