Control file for simulate (2)

######################## 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 simulate some sequences set this field to 'no'
Retrieve the name of the model's parameters = no

#the file with the user-specified parameters of the substitution model
Model parameters file = data/simulate.model

#Initialise the random number generator with a seed
Random seed = 1

#Random tree or user-specified tree ?
Random tree = yes

#parameters used if a random tree is generated
Number of species = 8
Maximum branch length = .5

#if Random tree == yes the tree will be saved with that file name
#if Random tree == no the tree is read from that file
Tree file = simulated-data/random-8species.tree

#generate sequences:
#for each model you have to specify the desired number of symbols
#if you are not using a MIXED model fill this field for the class 1 only
Number of symbols from class 1 = 600
Number of symbols from class 2 = 1200

#if you need a secondary structure fill the following fields
Structure for the elements of class 1 = .
Structure for the elements of class 2 = ()

#to produce a complete PHASE input file, you have to specify the type and the
#final length yourself
Data file type = RNA
Total length of the raw sequences = 3000

#the name of the file where your sequences are saved, please check this file
#before use
Output file = simulated-data/simulated-8species.mix