The MIXED model

Since the current trend in phylogenetic analysis is to use several genes and/or several sorts of sequences at once, models were designed for combined analyses of heterogeneous sequence data from the same set of species (Yang, 1996). PHASE allows to use multiple substitution models simultaneously to treat this kind of sequences, each model having its own independant set of parameters. The average mutation rate of the first model is still set to 1.0 but the average mutation rate of the others are now free parameters of the model. The MIXED model for combined analysis of heterogeneous data is equivalent to the model with proportional branch lengths described in Yang (1996).