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[http://www.ncbi.nlm.nih.gov/pubmed/19389736 This paper] claims to be interface equivalent, and more memory efficient. See http://compbio.cs.princeton.edu/mems
Text replace - "Alignment" to "Sequence alignment"
|sw summary=MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Basically it is a ultra-fast alignment of large-scale DNA and protein sequences
|bio domain=Genomics, Transcriptomics,
|bio method=AlignmentSequence alignment, Read mapping, |bio tech=any,Any
|created by=Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL
|created at=The Institute for Genomic Research(TIGR) and the Center for Bioinformatics and Computational Biology at the University of Maryland, MarylandCollege Park. Now maintained at the Center for Computational Biology, Johns Hopkins University
|maintained=Yes
|email address=salzberg@jhu.edu
|input format=FASTA,
|output format=delta
|licence=Artistic License,
|os=Linux,
}}
MUMmer is released as a package providing an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.
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. The original MUMmer system, version 1.0, is described in our 1999 Nucleic Acids Research paper. Version 2.1 appeared a few years later and is described in our 2002 Nucleic Acids Research paper, while MUMmer 3.0 was recently described in our 2004 Genome Biology paper.
[http://www.ncbi.nlm.nih.gov/pubmed/19389736 This paper] by another research group claims to be interface equivalent, and more memory efficient. See http://compbio.cs.princeton.edu/mems