To cite Geneious R11 and earlier in your paper, please use the following in the Methods section:
"Geneious x.x.x (where x.x.x is the version you are using) (https://www.geneious.com)".
To Cite Geneious Prime in your paper, please use the following in the Methods section:
"Geneious Prime 20XX.x.x (where 20XX.x.x is the year/version you are using).(https://www.geneious.com)" .