Control file for mlphase (2)

####################### The Data 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              = 1
{\DATAFILE}

######################## The Evolutionary Model Section ############
{MODEL}
#model : RNA7A + dG3
Model = RNA7A
Discrete gamma distribution of rates = yes
Number of gamma categories  = 3
{\MODEL}


####################### The Function Section ###########################
{FUNCTION}
Function = Search for ML topology

#Monophyletic clades ?
User defined monophyletic clades = yes
Clade file = data/primates.clades

#The search method for tree topology :
# 'Simple exhaustive search', 'Branch-and-bound exhaustive search' or
# 'Heuristic stepwise addition'
Topology search = Branch-and-bound exhaustive search

#optimise the substitution model parameters simultaneously ?
Optimise model parameters = yes

#a field to choose initial model parameters, this field is compulsory if
#the previous field is set to no
#### User's model parameters file = 

{\FUNCTION}

# Random seed for the random number generator
Random seed    = 2

# The next control line sets the output file
Output file = results/primates-rna-ml/primates-rna-ml.output