Control file for mlphase (1)

####################### The Data Section ###########################
{DATAFILE}
#The name of your data file 
Data file = data/hiv.dna

#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 : REV + dG4
Model = REV
Discrete gamma distribution of rates = yes
Number of gamma categories  = 4
{\MODEL}


####################### The Function Section ###########################
{FUNCTION}
Function = Optimise user-defined phylogenetic trees

#The file with the trees
Trees file = data/hiv-dna.trees
#The number of trees in this file
Number of trees = 2

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

# The name of the file containing initial substitution model parameters,
# if the previous field is set to no (ie, fixed parameters for the model) this
# field is compulsory
#### 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/hiv-dna-ml/hiv-dna-ml.output