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:
Other MUMmer programs may be found in the directory
where VER is the module version of MUMmer you are using.