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 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

Gowri-Shankar Vivek 2003-04-24