Effect of Coverage and Noise on Performance. (a), (b): Performance of MOPHY in capturing the underlying evolutionary distances between simulated networks with respect to coverage (fraction of modules that are used in phylogeny reconstruction). (a) Most specific modules, (b) most comprehensive modules. (c): The effect of noise and missing interactions on the performance of MOPHY. Even when the data is perturbed with 50% noise, MOPHY's accuracy in reconstructing the phylogeny is statistically significant. If the missing interactions are correlated across species, then the effect of missing data is comparable to that of random noise. On the other hand, if they are uncorrelated, then the performance of MOPHY is degraded more quickly, which is expected since the networks break apart in different ways in different species.