4.4 BppMixedLikelihoods: Bio++ Site-Likelihoods Inside Mixed Models.

The BppMixedLikelihoods program uses the common syntax introduced in the previous section for setting the alphabet, loading the sequences (see Sequences) and tree (see Tree) and specifying the model (see Model).

Given a mixed parameter name of mixed model, or a mixed model made of several models, the BppMixedLikelihoods program computes site per site log-likelihoods of the several values of the parameter, or of the several sub-models of the mixture. If the mixed model is built on a parameter which value follows a distribution, and in an additional column – named "mean" – the a posteriori mean value of the paramater is computed.

Specific options are:

output.likelihoods.file = {{path}}

Ouput file of the program (site specific log-likelihood, and mean of the mixed parameters, if any).

likelihoods.model_number = {integer}

In case of a non-homogeneous modeling, the number of the mixed model which parameter or sub-models are considered.

likelihoods.parameter_name = {string}

If the considered mixed model is built from a distribution on a parameter, the name of the parameter to be considered. In this case, an additional column is written, in which the average a posteriori value of the parameter is.