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Mauve is a program to align multiple genomes.


What it does:

  • aligns genomes and identifies homologous blocks
  • these are likely from a common ancestor or gained via horizontal transfer
  • blocks may have moved or been inverted in the genome

Mauve - align three strains

We will align three genomes of Streptococcus pneumoniae.

Open Mauve.

  • Go to File: Align with Progressive Mauve


  • Add Sequence

  • select the sequence(s). Use .fasta or .gbk files.

  • if using a reference sequence, add that first.

  • Align


  • Specify a name for the alignment.

  • Save

A console window will open and show the progress of the run.


When finished, the alignment will open:


  • Each row is a genome. Each coloured block is genetically similar.
  • If you are using annotated genomes, zoom in (with the magnifying glass) to see annotations.

For a different view, go to View: Style: Solid LCB colouring


  • Click on a block to align all genomes around that block.
  • The blue block is inverted in genome 3 (i.e., the reverse complement).

Mauve - align two assemblies from the same sample

In this example, we will align two genomes from the same sample that have been assembled with different tools.

  • Genome 1: Assembled from long reads; corrected with short reads.
  • Genome 2: Assembled from short reads.

Align the genomes:

  • Go to File: Align with Progressive Mauve
  • Add sequences. Add the long-read assembly sequence first.
  • Align
  • Name
  • Save

View the alignment:


Genome 2 has many contigs as it has been assembled using short reads.

  • These have been laid out in the order in which they appear in the file.
  • We need to re-arrange these contigs to align with the reference genome (Genome 1).

Re-order the contigs in Genome 2:

  • Go to Tools: Move Contigs
  • Specify output folder
  • Add sequences (add the long-read assembly first)
  • Start

The Mauve Console window will show the progress.

The re-ordered contigs will then be displayed:


Most of the contigs in Genome 2 can be aligned to one (red) section of Genome 1.