Figure 9

Generation of sample-consistent ARG with SC-sample. A) Generation of a binary tree is consistent with the left site. B) Determine whether the current local tree is consistent with the second site, the answer is yes since there is only one mutant edge. C) Determine whether the current local tree is consistent with the third site. This tree is not consistent because there are two mutant edges, so P₁ = 0.5. D) Generate the next recombination point that is uniform on [0, P₁] and obtain P₂ = 0.4. The dotted lines are the branches onto which the new branches are supposed to coalesce. E) The new branch coalesces and the [0, 0.4] part of the ARG is simulated.