Aligning whole genomes using Mauve

This tutorial covers the use of the Mauve whole genome aligner in Geneious Prime. You will learn to perform a basic alignment of complete bacterial genomes, order a draft genome against a reference, work with the Mauve viewer, and convert a Mauve alignment into a standard alignment for downstream analysis.

Mauve is developed and maintained by Aaron Darling at the University of Technology, Sydney. The program is designed for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. For further information about Mauve including a full user guide, please see the Mauve website.

This tutorial requires the Mauve plugin version 1.1.1 or above, running in Geneious 11.1, Geneious Prime 2019 or above. To install the Mauve plugin, go to Tools→Plugins, select Mauve from the list of Available Plugins and click Install. You will then need to restart Geneious before you can use the plugin.

Exercise 1: Alignment of complete bacterial genomes
Exercise 2: Aligning draft genomes
Exercise 3: Converting a Mauve alignment into a standard alignment

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