MAFFT
Fast and accurate multiple sequence alignment with MAFFT
Requires Geneious 2020.0+
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 two or more sequences and clicking on Align/Assemble - Multiple Align in the toolbar. MAFFT is available as an option at the top of the Alignment options window.
1.5.0 (14 Jul 2022) – Download for Geneious 2020.0
– Update MAFFT to 7.490
– Removed support for MAFFT under win32
1.4.0 (22 Oct 2019) – Download for Geneious 10.0
– Update MAFFT to 7.450 (7.429 for Window 32-bit) – fixes issues running MAFFT on Windows when paths contain non-Latin-1 characters
– Add support for using multiple threads (–thread -1)
1.3.7 (13 Feb 2018) – Download for Geneious 10.0
– Update MAFFT to 7.388 – fixes issues running MAFFT on Windows when plugin is installed by an administrator
1.3.6 (04 May 2017) – Download for Geneious 9.0
– Handle out of memory error gracefully instead of with crash
– Update binary to 7.308/7.309
1.3.3 (14 Oct 2013) – Download for Geneious 7.0
– Handle network file paths on Windows
– Add option to automatically determine sequences’ direction
– Fix error in Windows 64 version handling of spaces in data directory path
1.3 (25 Jan 2013) – Download for Geneious 5.0
– Updated binary to 7.017
Katoh, Standley 2013 (Molecular Biology and Evolution30:772-780) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. (outlines version 7)