Mauve Alignment in Geneious Prime

This Mauve alignment series shows how to align whole bacterial genomes with progressive Mauve in Geneious Prime, interpreting locally collinear blocks and inversions, then order draft genome contigs against a reference with the Mauve Contig Mover plugin, and convert the alignment into a standard format for phylogenetic tree building. The series spans three videos, 3 to 4 minutes each.

Course Content

Align Whole Genomes with Mauve

Align three whole genomes using progressive Mauve in Geneious Prime, then explore locally collinear blocks (LCBs) and inversions in the Mauve viewer. Adjust the LCB weight slider, or click Allow Editing to create a standard alignment copy.
LENGTH 4 minutes

Align Draft Genomes with Mauve

Order a draft genome’s contigs against a reference using the Mauve Contig Mover (MCM) algorithm, which Geneious selects by default for sequence lists. Compare the result to a progressive Mauve alignment to see why MCM gives fewer, cleaner LCBs.
LENGTH 4 minutes

Convert Mauve Alignment to Standard Alignment

Convert a Mauve genome alignment into a standard alignment using Extract Mauve Regions, then Concatenate Sequences or Alignments by index when sequence names differ slightly. Rearranged genomes lose their rearrangement information in the process.
LENGTH 3 minutes

Recommended Resources

Plugin - Install Mauve

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

Why is my alignment taking so long?

How to choose the appropriate alignment algorithm for your dataset.

Manual for the Mauve Aligner

A guide to aligning bacterial genomes with Mauve in Geneious.

Manual for Installing Plugins

A guide extending to the functionality of Geneious Prime by installing plugins.

More Geneious Academy

TUTORIALHow to Align Genomes with Mauve in Geneious Prime
Align three M. tuberculosis complex genomes with Mauve, then order a draft assembly against a reference.
Read Tutorial
VIDEO SERIESPhylogenetic Trees in Geneious Prime
Align your sequences and build distance, maximum likelihood, or Bayesian phylogenetic trees, then customize and explore them in the tree viewer.
Watch Series
VIDEO SERIESMultiple Alignments in Geneious Prime
Choose the right alignment algorithm for your dataset size, from Muscle to MAFFT, then align multiple sequences and assess homology in Geneious Prime.
Watch Series
VIDEO SERIESAnnotate Sequences in Geneious Prime
Annotate sequences in Geneious Prime by importing files, transferring or copying annotations between homologs, using a database, or annotating by BLAST.
Watch Series
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