Versatile and open software for comparing large genomes
Open accessAbstract
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 .
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MUMmer 3.0 uses all maximal matches, including non-unique ones, to align two genomes.
“To overcome this problem, the new MUMmer 3.0 uses all maximal matches including non-unique ones to align the two genomes [19].”
From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [19]
The Results section (“Non-unique maximal matches”) says MUMmer 3.0 can find all maximal matches, including non-unique ones, between two sequences. It specifies that this requires a command-line option; the claim presents it as what MUMmer 3.0 uses without that qualification. (LLM, conf=0.86)
Experimental — accuracy not yet measured
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- Authors
- Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L.
- Affiliations
- Universität Hamburg (DE)
- University of Virginia (US)
- Corresponding author
- Salzberg, Steven L
- Venue
- Genome Biology
- Published
- 2004-01-30
- Volume
- 5
- Issue
- 2
- Pages
- R12-R12
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC395750
- OpenAlex
- W2107282968
- Cited by
- 5,254
- References
- 6
- Citations by year
- 2026: 208 · 2025: 245 · 2024: 319 · 2023: 302 · 2022: 370 · 2021: 526 · 2020: 455 · 2019: 383 · 2018: 348 · 2017: 327 · 2016: 255 · 2015: 237 · 2014: 248 · 2013: 240 · 2012: 164
- FWCI
- 17.44
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, other-oa)
- PubMed (publishedVersion)
- University Libraries (University of Maryland) (submittedVersion)
- Funders
- National Science Foundation (0114792)
- University of Virginia
- Deutsche Forschungsgemeinschaft
- National Institutes of Health (n01ai15447-36-0-3)
- National Institute of General Medical Sciences (T32GM008715)
- National Institute of Allergy and Infectious Diseases (N01 AI015447)
- U.S. National Library of Medicine (R01LM006845)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- mummers, genome alignment, eukaryotic genomes, open source software, sequence alignment
- MeSH terms
- Animals, Anopheles, Computer Graphics, Drosophila, Humans, Software, Genome, Human, Sequence Alignment, Genome, Genome, Fungal, Genomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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