Control file for

######################## The Evolutionary Model Section ############ {MODEL} #the name of your model Model = MIXED #since we are using the mixed model we provide the number of models Number of models = 2 {MODEL1} #DNA model : REV + dg3 Model = REV Discrete gamma distribution of rates = yes Number of gamma categories = 3 {\MODEL1} {MODEL2} #RNA model : RNA7A + dg4 + I Model = RNA7A Discrete gamma distribution of rates = yes Number of gamma categories = 4 Invariant sites = yes {\MODEL2} {\MODEL} ######################## The Simulate Section ############ #to produce an example of '.model' file for the specified model set this field #to 'yes' Retrieve the name of the model's parameters = yes #the following field is the name of the '.model' file to create Model parameters file = data/simulate.model

Gowri-Shankar Vivek 2003-04-24