MUMmer

MUMmer is a bioinformatics software system for aligning genome sequences of any length to one another, and it has been widely used for comparing different genomes to one another. It is based on the suffix tree data structure and is one of the fastest and most efficient systems available for this task. The acronym "MUMmer" comes from "Maximal Unique Matches", or MUMs.

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The MUMmer software is open source and can be found at The MUMmer home page. The home page also has links to technical papers describing the system. The system is maintained primarily by the bioinformatics group at the Center for Bioinformatics and Computational Biology at the University of Maryland.