Install the plugin by downloading the gplugin file and dragging it in to Geneious Prime or use the plugin manager in Geneious Prime (under Tools - Plugins in the menu).
Once installed, run the plugin by selecting a multiple sequence alignment and clicking on Tree in the toolbar. PhyML is available as an option at the top of the Tree building options window.
2.2.4 (06 Mar 2019) – Download for Geneious 10.0
– Updated included PhyML to version 3.3.20180621
– Show PhyML version number in the options dialog
2.2.3 (27 Mar 2017) – Download for Geneious 6.0
– Fixed crash on Windows when running from a data directory containing certain non-Latin characters (e.g., Chinese)
– Fixed crash that would occur when running with a custom substitution model on Windows machines
2.1.0 (29 Jun 2012) – Download for Geneious 5.1
– Added custom substitution model option, can be used with ModelTest output
– Added optimization option (Topology/Length/Rate)
"New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0." Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. Systematic Biology, 59(3):307-21, 2010.