Fig. 4
Simulation plots. We plot the proportion of combinations simulated, that belong to the profile {AA, CC}, against d/s ratio along different branch lengths (a for 0.1; b for 0.5; c for 1; d for 5). Each box plot is obtained by varying the r 1 and r 2 rates within the range [1,100] and by randomly picking an ancestral state from the frequency vector issued from the matrix Q