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Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics. Aligning whole genomes is a fundamentally different problem than aligning short sequences.

Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours.

Required Modules


  • mauve

System Variables


Additional Information

See using mauve from the command-line on how to use Mauve at the command line. You can also briefly run the main Gui by logging into the server. See GUI_Programs for details on connecting to the gui server.

To run Mauve gui
Run 'export _JAVA_OPTIONS="-Xmx<MEMORY>"' where <MEMORY> is the maximum heap memory size to be used by Java for Mauve in Gigabytes (g) or Megabytes (m) before running 'Mauve'. This will override the initial setting of 500m. Examples of memory values in mega- or gigabytes: "1500m" or "2g".