Average posterior probability of the correct topology (for networks A and B, see Fig 7) obtained by running SnappNet on simulated data.

Results are given as a function of the number of sites and as a function of the hyperparameter values α and β for the prior on θ (θ ∼ Γ(α, β) and ). Here, one lineage was simulated per species. Constant sites are included in the analysis, the rates u and v are considered as known, and 20 replicates are considered for each simulation set up (criterion ESS > 200; , r ∼ Beta(1, 1), for the network prior).