Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).
Once installed, run the plugin by selecting a multiple sequence alignment and clicking on Detect Recomb. in the toolbar. The results are presented as a set of the most probable tree topologies along with graphs displayed inside the Alignment view tab.
Minin VN, Dorman KS, Suchard MA. Dual multiple change-point model leads to more accurate recombination detection, Bioinformatics, 21:3034-3042, 2005.