Thank you for installing the Geneious PhyML plugin.
The PhyML tree builder is available when you click "Tree" in the toolbar at the top of Geneious.

If you use PHYML, please cite:
"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood."
Guindon S, Gascuel O.
Systematic Biology. 2003 52(5):696-704.
This is a detailed description of the algorithm. This is also a "Fast Breaking Paper".