Bootstrap support values for equidistant trees. All five ancestral sequences were combined for a given scenario. (a) Boxplot and solid splines are for 14 taxa scenarios of the three methods. Dashed lines and dotted lines are splines of ten and 18 taxa, respectively. (b) Direct comparison of the 14 taxa splines and medians of all three methods. Sample sizes are 7,000, 11,000 and 15,000 for each of the ten, 14 and 18 taxa scenarios, respectively. Splines show a decrease of robustness with increased number of taxa used and increased branch lengths. Secondary structure and doubled sequences show an improvement in robustness in contrast to normal sequence information.