Figure 1.
Scheme of the analysis. For most taxa we can reliably predict the outgroup (top). In this case, only the changes taking place in each of the terminal leaves of the ingroups are counted (thick lines), and only if there were no changes in the same position elsewhere in the tree, that is, if all other nucleotides in the same position are strictly identical. The table contains the sum of all substitutions of each type. When there is no single outgroup, or it cannot be reliably predicted, the analysis is done on all terminal branches of the tree (bottom). A substitution is marked if it only occurred in that branch of the tree.
