MUMmer protocols

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MUMmer statistics

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Associated diseases

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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



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  • 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 in pipelines

PMCID: 5755439
PMID: 29304732
DOI: 10.1186/s12864-017-4421-z

[…] non-coding rnas were blasted and annotated via pfam software and database. colinearity between the genomes of p. tuoliensis and p. eryngii var. eryngii (atcc90797, jgi) was analyzed by using mummer version 3.1 [] with different settings, i.e., mincluster = 2000 for the whole genome comparison and mincluster = 1000 for the scaffold., 2b–rad libraries were prepared and analyzed […]

PMCID: 5793183
PMID: 29324691
DOI: 10.3390/genes9010031

[…] contigs. we then determined the coverage level at 50% of the total cumulative assembly length; half of that coverage level was selected as a coverage filter. the remaining reads were aligned with nucmer [] against the complete genome sequence of arthrobacter sp. hiyo8 dna (accession number ap014719.1), which was the closest taxonomic relative determined by a blast of the 16s rrna sequence. […]

PMCID: 5797428
PMID: 29434576
DOI: 10.3389/fmicb.2018.00028

[…] five runs of iontorrent sequencing (use of gc% and reads coverage from iontorrent pgm reads) (; ). the new assembly confirmed the previous version as all nine contigs from the previous aligned with mummer to the largest of the two contigs, except for a ca. 21 kb region we had not manually selected using differential coverage binning because of a variable read coverage between runs. […]

PMCID: 5798813
PMID: 29423234
DOI: 10.1038/s41438-017-0011-0

[…] assemblies were plotted., all four pepper assemblies and the solanum lycopersicum version 3.0 (tomato) were aligned against each other in a pairwise fashion for all pseudochromosome sequences using mummer version 3.23. the nucmer alignment algorithm was utilized requiring minimum clusters of 100 bp with maximum gap of 500 bp. these results were then filtered for the within-pepper comparisons […]

PMCID: 5824051
PMID: 29237792
DOI: 10.1128/JCM.01384-17

[…] and animals with identical core genomes were extracted using an inhouse r script. ani was calculated by performing pairwise comparison of genome assemblies of these c. difficile rt078 strains using mummer ()., antimicrobial resistance genes were identified within the c. difficile rt078 genomes through comparison to the card database with the ariba (antimicrobial resistance identification […]

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MUMmer in publications

PMCID: 5955891
PMID: 29769695
DOI: 10.1038/s41598-018-26073-5

[…] 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 […]

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

[…] on the genome of neurospora crassa. all other parameters were left 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 […]

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

[…] integer value before being plotted 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 […]

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., we assessed the completeness of our assembly […]

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

[…] 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 […]

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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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