Control file for mcmcphase (2)

######################## The Sequence Alignment Section ############
{DATAFILE}
Data file = data/mammals69.mix
Interleaved data file = no
Outgroup              = 26
{\DATAFILE}

######################## The Evolutionary Model Section ############
{MODEL}
Model = MIXED
Number of models = 2
{MODEL1}
    Model = REV
    Discrete gamma distribution of rates = yes
    Number of gamma categories  = 4
    Invariant sites             = no
{\MODEL1}
{MODEL2}
    Model = RNA7A
    Discrete gamma distribution of rates = yes
    Number of gamma categories  = 4
    Invariant sites             = no
{\MODEL2}
{\MODEL}

######################## The MCMC PERTURBATION Section ############
{PERTURBATION}
#PERTURBATION OF THE TREE :
Initial branch step proposal parameter = 0.03
Branch length upper bound = 1.7

#PERTURBATION OF THE MODEL :
Model 1 priority = 8
Model 2 priority = 24

Average rates, proposal priority = 1
Average rates, initial step = .3
Average rates, proposal minimum acceptance rate = .15
Average rates, proposal maximum acceptance rate = .20

{PERTURBATION1}
    Frequencies, proposal priority = 1
    Rate ratios, proposal priority = 1
    Gamma parameter, proposal priority = 1
{\PERTURBATION1}
{PERTURBATION2}
    Frequencies, proposal priority = 1
    Rate ratios, proposal priority = 1
    Gamma parameter, proposal priority = 1
{\PERTURBATION2}

{\PERTURBATION}

Random seed = 1

Burnin iterations = 40000

Sampling iterations = 100000

Sampling period = 10

Random start model parameters = no
User's starting model parameters file = data/mammals69-mix-consensus.model

Random start tree = no
User's starting tree file = data/mammals69-mix-consensus.tree

Output file   = results/mammals69-mix-mcmc/mammals69-mix-mcmc-preinit
Output format = phylip