** Next:** Bayesian phylogenetics
** Up:** Refinements to substitution models
** Previous:** Invariant and discrete gamma
** Contents**

##

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).

Gowri-Shankar Vivek
2003-04-24