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.