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 - 

Display tree in new window - 

Display tree with alignment editor - 

Synchronize alignment with tree - 

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.