MUMmer

Application data
Created by	Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL
Biological application domain(s)	Alignment
Principal bioinformatics method(s)	Alignments
Created at	The Institute for Genomic Research, Maryland
Maintained?	Maybe
Input format(s)	FASTA
Operating system(s)	POSIX

Summary: MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence.

"Error: no local variable "counter" was set." is not a number.

[PMID http://www.ncbi.nlm.nih.gov/pubmed/19389736] claims to be interface equivalent, and more memory efficient.

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. For more information regarding the MUMmer package, please refer to the: