Versatile and open software for comparing large genomes
Genome biologyPublished 30 January 2004Open access
Stefan Kurtz, Adam M. Phillippy, Arthur L. Delcher, Michael Smoot, Martin Shumway, Corina Antonescu
Citations5,846
SJR quartileQ1
SJR score5.71
SNIP2.21
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TL;DR
The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes.
Abstract
The newest version of MUMmer easily handles comparisons of large eukaryotic genomes at varying evolutionary distances, as demonstrated by applications to multiple genomes. Two new graphical viewing tools provide alternative ways to analyze genome alignments. The new system is the first version of MUMmer to be released as open-source software. This allows other developers to contribute to the code base and freely redistribute the code. The MUMmer sources are available at http://www.tigr.org/software/mummer.
Keywords
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Proceedings of the National Academy of SciencesImproved tools for biological sequence comparison.
11,334 Citations1988William R. Pearson, David J. Lipman
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Journal of Molecular BiologyIdentification of common molecular subsequences
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