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The Building Phylogenetic Tree dialog for the PhyML Maximum Likelihood method has the following view:

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There following parameters are available:

Substitution model parameters:

Substitution model - 

Equilibrium frequencies - 

Transition/transversion ratio - 

Proportion of invariable sites - 

Number of substitution rate categories - 

Gamma shape parameter - 

Branch support parameters:

Use fast likelihood method - 

Perform bootstrap - 

Tree searching parameters:

Make initial tree automatically - 

Type of tree improvement - 

Set number of random starting tree - 

Optimize topology - 

Optimize branch lengths - 

Gamma — sets the number of rate categories for the gamma distribution.

You can select the following parameters for the MCMC analisys:

Chain length — sets the number of cycles for the MCMC algorithm. This should be a big number as you want the chain to first reach stationarity, and then remain there for enough time to take lots of samples.

Subsampling frequency — specifies how often the Markov chain is sampled. You can sample the chain every cycle, but this results in very large output files.

Burn-in length — determines the number of samples that will be discarded when convergence diagnostics are calculated.

Heated chains — number of chains will be used in Metropolis coupling. Set 1 to use usual MCMC analysis.

Heated chain temp — the temperature parameter for heating the chains. The higher the temperature, the more likely the heated chains are to move between isolated peaks in the posterior distribution.

Random seed — a seed for the random number generator.

Save tree to — file to save the built tree.

Press the Build button to run the analysis with the parameters selected and build a consensus tree.