Control file for optimise

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

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

#the species used to root the tree
Outgroup              = 14
{\DATAFILE}

######################## The Evolutionary Model Section ############
{MODEL}
#model : RNA16A + dG4
Model = RNA16A
Discrete gamma distribution of rates = yes
Number of gamma categories = 4
{\MODEL}

####################### The tree & model Section ####################
#the phylogeny to optimise
Tree file = data/primates.tree

#an optional field to choose the initial model parameters (and check
#whether the method always converge to the same tree)
#Starting model parameters file = 

#a random seed to initialise the branch lengths randomly in case the phylogeny
#provided does not hold this information
Random seed = 1

#the base name of the three output files (base.output, base.model, base.tree)
Output file = results/primates-rna-optimise/primates-rna-optimise-RNA16A