Quartet distances 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. The samples size of each scenario is 1,000. The accuracy of tree topologies decreases with more taxa and greater evolutionary distances between sequences. Trees calculated with secondary structures or doubled sequences show greater accuracy than those determined with normal sequences.