Control file for likelihood

######################## The Sequence Alignment Section ############
{DATAFILE}
#The name of your data file
Data file = data/mammals69.mix

#The format of your data file (interleaved or not)
Interleaved data file = no

#The species used to root the tree
Outgroup              = 26
{\DATAFILE}

######################## 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

#and we define each substitution model inside its own block.
#the file "data/mammals69.mix" is a RNA sequence with loops and stems
#we did not specify a class section but the code used was MIXED
#therefore the first model must be the DNA model for the loop
#and the second model must be the RNA model for the helices.
{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 tree & model Section ####################

#To evaluate the likelihood of a phylogeny you must provide
#1.a phylogeny file (tree with branch lengths)
Tree file = data/mammals69-mix-consensus.tree

#2.the parameters for the model you defined above
Model parameters file = data/mammals69-mix-consensus.model