The evolution of a set of orthologous bases along a phylogenetic tree. In the left panel the expression (77) is illustrated. For notational simplicity we write P
(w, t). The middle panel illustrates the recurion relations (78) with c and c' the children of node n, S
the set of bases in S that descend from c and S
the set of bases in S that descend from c'. The right panel shows expression (77) for a more complex selection pattern with branches evolving according to the WM in red, and those evolving to the background in black.