MUMmer is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure and is one of the fastest and most efficient systems available for this task, enabling it to be applied to very long sequences. It has been widely used for comparing different genomes to one another. In recent years it has become a popular algorithm for comparing genome assemblies to one another, which allows scientists to determine how a genome has changed after adding more DNA sequence or after running a different genome assembly program. The acronym "MUMmer" comes from "Maximal Unique Matches", or MUMs.

References:

• Delcher, A. L.; Kasif, S.; Fleischmann, R. D.; Peterson, J.; White, O.; Salzberg, S. L. (1999). "Alignment of whole genomes". Nucleic acids research 27 (11): 2369–2376. doi:10.1093/nar/27.11.2369. PMC 148804. PMID 10325427.
• Delcher, A. L.; Phillippy, A.; Carlton, J.; Salzberg, S. L. (2002). "Fast algorithms for large-scale genome alignment and comparison". Nucleic acids research 30 (11): 2478–2483. doi:10.1093/nar/30.11.2478. PMC 117189. PMID 12034836.
• Delcher, A.; Harmon, D.; Kasif, S.; White, O.; Salzberg, S. (1999). "Improved microbial gene identification with GLIMMER". Nucleic Acids Research 27 (23): 4636–4641. doi:10.1093/nar/27.23.4636. PMC 148753. PMID 10556321.

External links:

• MUMmer home page http://mummer.sourceforge.net/
• Manual: http://binf.gmu.edu/software/mummer/manual/#installation
• Examples: http://binf.gmu.edu/software/mummer/examples/

示例： promer -p promer D_melanogaster_2Rslice.fasta D_pseudoobscura_contigs.fasta