MAFFT

MAFFT Plugin

Fast and accurate multiple sequence alignment with MAFFT

Quick Start

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.

History

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

Citing

Katoh, Standley 2013 (Molecular Biology and Evolution30:772-780) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. (outlines version 7)

Links

• MAFFT Website