LASTZ
Align large genomes using LASTZ
Requires Geneious 7.0+

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 nucleotide sequences and clicking on Align/Assemble - Align Whole Genomes in the toolbar. LASTZ is available as an option at the top of the Alignment options window.
The results are presented as a collection of multiple alignments, one for each reference sequence with orthologous regions from the other sequences aligned to them. A dotplot is also displayed inside the Alignment view.
Harris, R.S. (2007) Improved pairwise alignment of genomic DNA. Ph.D. Thesis, The Pennsylvania State University.