Clustal Omega comes bundled with Geneious Prime 2020 and later. If you are using an older version please follow the instructions below to install the plugin.
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 two or more sequences and clicking on Align/Assemble - Multiple Align in the toolbar. Clustal Omega is available as an option at the top of the Alignment options window.
Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7:539 doi:10.1038/msb.2011.75