MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.  MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system.

To run this software interactively in a Linux environment run the commands:

module load mummer
mummer [options] input1.fasta input2.fasta > mummer.output
For a complete list of options, please visit the MUMmer homepage, or use the command:
mummer -h
Other MUMmer programs may be found in the directory
where VER is the module version of MUMmer you are using.
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