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MUMmer specifications


Unique identifier OMICS_14554
Name MUMmer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data Generates an image showing the alignment of a set of contigs to a reference chromosome.
Output format FIG, PDF
Operating system Unix/Linux, Mac OS
Programming languages C, C++, Java, Perl, Python, Ruby
License Artistic License version 2.0
Computer skills Advanced
Version 4
Stability Beta
Make, perl, sh, csh, g++, sed, awk, ar, fig2dev, gnuplot, xfig
Maintained Yes


  • mummerplot
  • NUCmer




No version available



  • person_outline Guillaume Marçais
  • person_outline Steven Salzberg
  • person_outline Aleksey Zimin

Additional information The older versions of MUMmer are available at

Publications for MUMmer

MUMmer citations


Genomic and functional characterisation of IncX3 plasmids encoding blaSHV 12 in Escherichia coli from human and animal origin

Sci Rep
PMCID: 5955891
PMID: 29769695
DOI: 10.1038/s41598-018-26073-5
call_split See protocol

[…] rarchically clustered and displayed as a phenogram using the BioNJ algorithm, where the underlying distance matrix was calculated from the pairwise non-overlapping maximal unique matches (MUMs) using Nucmer version 3.07,. Relative pairwise distances were obtained by dividing the pairwise MUMs’ sum by the average genome size of the two paired genomes (MUMi genomic distance). BioNJ trees were genera […]


Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] ted with the number of occurrences and level of density using R v3.1.3 ( The Harpellales genome dot plot comparisons were generated using the MUMmer (v3.23) package (). The “nucmer” algorithm and the “delta-filter” function were employed to find the reciprocal best matches between the genome scaffolds. Total numbers of matches and aligned bases were calculated using the “ […]


Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast

BMC Genomics
PMCID: 5952469
PMID: 29764372
DOI: 10.1186/s12864-018-4751-5

[…] at default values.Pairwise alignments of genomes A, C and D (discarding all contigs shorter than 25 kBp) were calculated with the nucmer algorithm, as implemented in Mummer 3.23, and plotted with the mummerplot utility [] as described by Hane et al. [].The differences between the subgenomes of diploid H. werneckii strains (as a measure of heterozygosity within the genomes) were calculated by separ […]


Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution

BMC Genomics
PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] genome using 3854 ultraconserved elements (UCEs) that were generated by sequence capture from the same individual []. The UCE sequences were aligned against the masked Bambusicola assembly using the NUCmer program [] from MUMmer [] with default settings. We extracted coverage and mismatch information for each UCE from the pairwise alignments. […]


Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats

PLoS One
PMCID: 5940233
PMID: 29738547
DOI: 10.1371/journal.pone.0196995

[…] astid genes as a reference (i.e. Chondrus crispus, Calliarthron tuberculosum) [, ]. After the reassembly process, we obtained the circular plastid genomes and those circular genomes were confirmed by MUMmerplot [] and by comparing with reference genomes to check for completeness. The sequences were verified with read-mapping tools implemented in CLC Genomics Workbench to correct for any sequencing […]


Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)

Front Plant Sci
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] al., ). Genomic sequences were first aligned annotated genes based on amino acid sequence using Promer package of Mummer (version 3.22) (Delcher et al., ). Whole genome dot plots were generated using Mummerplot (Delcher et al., ) and Gunplot 5.0 ( Ks values of the homologs within collinearity blocks were calculated using the perl script, included […]


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MUMmer institution(s)
Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA; Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA; Center for Computational Biology, Johns Hopkins School of Medicine, Baltimore, MD, USA; National Human Genome Research Institute, Bethesda, MD, USA; Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, USA
MUMmer funding source(s)
Supported in part by the U.S. National Institutes of Health under grant R01 GM083873, in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grant GBMF4554, and in part by National Science Foundation Grants IOS-1238231, IOS-144893.

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