Control file for

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

Gowri-Shankar Vivek 2003-04-24