...
Number of substitution rate categories - a number the number of substitution rate categories.
...
Branch support parameters - a the selection of the method that is used to measure branch support:
...
Tree searching parameters - a the selection of the tree topology searching algorithm:
...
Set number of random starting tree - a the number of random starting tree.
Optimize tree topology - the tree topology is optimised in order to maximise the likelihood.
Optimize branch lengths - optimize branch lengths.
Optimise substitution rate - substitution rate parameters are optimized.
Display tree in new window - displays tree in the new window.
...