Control file for mcmcphase

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 user-specified model parameters. Otherwise the sequences are used to initialise the substitution model.
Random start model parameters = no
User's starting model parameters file = data/primates-RNA7A.model

Random start tree and User's starting tree file: similarly, one can choose to initialise the chain randomly or with a user-defined topology. We do not encourage the use of an initial user-defined 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/hiv-dna

Output format: the format used for the topologies in the .samples file, it can be phylip (with a semi-colon at the end) or bambe (without semi-colon).
Output format = phylip