Mixed model for combined analyses of heterogeneous data

To study heterogeneous sequences several models are required. The mixed model allows these models to work concurrently.

Model: this field contains the name of the model which is MIXED.
Model = MIXED

Number of models: the number of models used concurrently. If a class section was provided with the data file then the number of models should be the same as the number of classes. If you used the flag MIXED in your data file and did not provide a class section then this parameter has to be set to 2 and the two models must be a DNA substitution model and a base-paired substitution model respectively.
Number of models = 3

{MODELi} block: each model used in the mixed model must be defined in its own block. If the number of models is n then the MODEL block must contains n blocks whose name are MODEL1, MODEL2, ..., MODELn. The content of these blocks is the same as for a simple substitution model block.

{MODEL}

Model = MIXED

Number of models = 2

{MODEL1}

Model = REV

Invariant sites = yes

{$\backslash$MODEL1}

{MODEL2}

Model = RNA7A

Discrete gamma distribution of rates = yes

Number of gamma categories = 5

{$\backslash$MODEL2}

{MODEL3}

Model = RNA7D

Invariant sites = no

Discrete gamma distribution of rates = no

{$\backslash$MODEL3}

{$\backslash$MODEL}