Distribution of normalized RF distances (500 simulations) for the simulation settings S, c, E, n and S, m, E, n. The reconstructed trees were compared with the model tree via the RF distance (see methods for details). The distributions resulting from 500 repetitions are shown. The boxes mark the 1/4- and 3/4-quantiles, the vertical line with the notches is the median with the 95% confidence intervall for comparing two medians. The vertical line without the notches is the mean of the data. The vertical black line drawn throughout the diagrams is the mean RF distance of all complete gene trees, which serves as the baseline distance.