Fig. 1

Transition probabilities in a simplified world. Comparison between the transition probabilities in a sequence with constant substitution rate over sites and in a sequence with two equiprobable classes of rates for a simplified system described in Results. Black: P _AB (t) (solid line) and \(\tilde {P}_{AB}(t)\) (points); Blue: P _AC (t) (solid line) and \(\tilde {P}_{AC}(t)\) (points); Red: P _BC (t) (solid line) and \(\tilde {P}_{BC}(t)\) (points)