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Please see the examples provided in
appendix A.7 and A.8.
In the control file of mcmcphase one can/must have:

a DATAFILE block: see the data file block section.

a MODEL block: see the model block section.

a PERTURBATION block: control block for the mixing properties of mcmcphase (see
below).

Random seed: the seed for the random number generator.
Random seed = 1

Burnin iterations: the number of ``burnin'' cycles (i.e.,
cycles before the beginning of the sampling).
During the ``burnin'', only likelihood values are stored.
Burnin iterations = 150000

Sampling iterations: the number of cycles for sampling.
Sampling iterations = 600000

Sampling period: the number of cycles between extraction of two consecutive samples.
Sampling period = 20

Random start model parameters and User's starting model parameters file: to reduce the
necessary ``burnin'' time, the chain can be initialised with some userspecified model parameters. Otherwise
the sequences are used to initialise the substitution model.
Random start model parameters = no
User's starting model parameters file = data/primatesRNA7A.model

Random start tree and User's starting tree file:
similarly, one can choose to initialise the chain randomly or with a userdefined topology.
We do not encourage the use of an initial userdefined topology but this option
can be useful to quickly gain an idea of what results can be expected.
Random start tree = yes
User's starting tree file = this field is ignored in this case

Output file: the basename for all the output files (basename.besttree,
basename.bestmodel, basename.mp, basename.samples,
basename.bl, basename.output and basename.plot).
Output file = results/hivdna

Output format: the format used for the topologies in the .samples file,
it can be phylip (with a semicolon at the end) or bambe
(without semicolon).
Output format = phylip
Next: PERTURBATION block
Up: mcmcphase
Previous: Using consensus
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GowriShankar Vivek
20030424