Figure 11

Underestimate of ML branch lengths with fixed parameters. Percentage that branch lengths were underestimated for 1 kb 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 fixed model parameters, Depth 1 and depth 2 branches are shown separately (white and gray boxes respectively). Open circles are outliers.