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.

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Link: http://mummer.sourceforge.net/ Category: Alignment

[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.