Figure 6
From: Reconciliation and local gene tree rearrangement can be of mutual profit
The simulation protocol to obtain inferred gene trees from sequences derived from a true gene tree. The module “Deviation from ultrametricity” is taken from the program of Galtier that converts the edge lengths of ultrametric trees from the time unit into substitution numbers [36]. G ML denotes the initial gene tree inferred by Maximum Likelihood from the simulated sequences; Rec ML , resp. Rec R , denotes the reconciliation between G ML and the reference species tree predicted by Mowgli[2], resp. Ranger-DTL-D [3]; G NNI is the alternative gene tree found by MowgliNNI and Rec NNI is the reconciliation between G NNI and the species tree.