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 . G
denotes the initial gene tree inferred by Maximum Likelihood from the simulated sequences; Rec
, resp. Rec
, denotes the reconciliation between G
and the reference species tree predicted by Mowgli, resp. Ranger-DTL-D ; G
is the alternative gene tree found by MowgliNNI and Rec
is the reconciliation between G
and the species tree.