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MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. 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. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences. Template:App Location

Available versions

  • 3.22, 3.23 on RedHat EL6 nodes

Note: mummer requires the perl module to be loaded

Running the application using modules

To use mummer with the environment modules system at HPC the following commands are available:

Get module information for mummer:

$module spider mummer

Load the perl module:

$module load perl

Load the application module:

$module load mummer

or in one command:

$module load perl mummer

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_MUMMER_DIR - directory where mummer is located.
  • HPC_MUMMER_BIN - executable directory