Align multiple genomes to identify large-scale evolutionary events using Mauve

Mauve Plugin

Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics. Construct and visualize multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion using Mauve.

By Aaron Darling

Quick Start

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. Mauve is available as an option at the top of the Alignment options window.

The results are presented as a Mauve alignment document which displays the Mauve alignment view as a tab. This gives an overview of all genomes with related regions linked as colored blocks.


1.1.3 (15 Feb 2021) – Download for Geneious 2021.0

– Fixed a bug loading of annotations and contig boundaries for sequence lists missing accession numbers on contained sequences

– Updated some icons to be high res and fit the new UI

– Updated wording of “Show Details” in exception dialog

– Prevented creating or viewing invalid alignments

1.1.1 (30 Oct 2017) – Download for Geneious 11.0

– Fixed DCJ analysis in most cases

– Added an option to save contigs in order as a sequence list or concatenated sequence when running MCM

– Mauve alignment exporter now exports referenced source genomes in Genbank flat format (better supported by current versions of Mauve)

– Mauve .backbone file is now saved; when exporting Mauve alignments in .xmfa format the .backbone file will also be exported if it is available

1.1.0 (29 Sep 2017) – Download for Geneious 11.0

– For multiple input documents, sequence lists are now assumed to contain sequences from a single genome (a single input sequence list is still treated as a list of complete genomes)

– The MCM (contig reordering) algorithm is now available

– Updated to latest Mauve development snapshots: 2015-02-26 (Windows), 2015-02-25 (Mac OS), 2015-02-13 (Linux 64 bit)

– Fixed bug where track data (such as qualifiers used for heatmap coloring) wasn’t copied to the Mauve result

1.0.5 (10 Mar 2017) – Download for Geneious 6.0

– Fixed a problem where import fails on valid XMFA file when there is no space in front of sequence number

– Fixed the importer producing nameless documents

– Made the operation failed dialogues more friendly

– Fixed a problem that caused alignments extracted from features in the genome alignment viewer to be offset by 1

– Fixed a problem where question mark nucleotides were being deleted by Mauve and causing annotations to be offset

– Now mentions when no alignment could be produced

0.6.11 (05 Jul 2012) – Download for Geneious 5.6

Supports annotation tracks


Aaron E. Darling, Bob Mau, and Nicole T. Perna. 2010. progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss, and Rearrangement. PLoS One. 5(6):e11147.


Get started with Geneious today