MUMmer pipeline

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
Requirements 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 citations

PMCID: 5952926

[…] of illumina-generated sequences [24]. single nucleotide polymorphisms (snps) and short insertions/deletions (indels) were identified relative to the genome of strain ngas979 using vaal [25] and/or nucmer [26]. whole-genome and/or core genome snps were used to construct neighbor-joining phylogenetic trees (1000 bootstrap replications) using splitstree4 [27]. contigs were annotated with prokka […]

PMCID: 5520028

[…] single-copy phylogenetic marker genes as described previously (raveh-sadka et al., 2015; probst et al., 2016). de-replication of bins was determined using pairwise identity comparisons with nucmer (kurtz et al., 2004) via scripts described previously (probst et al., 2016)., alignment of 16s rrna genes with reference sequences from the silva ssu database v.123 was performed […]

PMCID: 5702742

[…] ntra-st case included the requirement that a sequence was present in all the genomes with an identity higher than 95%. single-nucleotide variant distribution within every subtype was calculated using nucmer (kurtz et al., 2004) pipeline for computing pairwise alignment and snv reporting. for st1 the average pairwise alignment was 3 431 933 bp (s.d. 2 323 310 bp), for st2 3 876 563 bp (s.d. 1 985 7 […]

PMCID: 5712208

[…] pathway was manually constructed and cross-checked with cited published reviews/papers. the blast analysis of the putative phenazine gene cluster against other genomes was performed using mummer 3.0 (kurtz et al., 2004). the image of the putative operon against genomes was produced using the blast ring image generator (brig) (alikhan et al., 2011). gene ontologies were analysed […]

PMCID: 4705583

[…] of the x. maculatus transcriptome. to build the transcriptomes of x. couchianus and x. hellerii, scaffold version genomes of these two query species were aligned to the x. maculatus genome using nucmer3.0 [24] with parameters implemented by rapid annotation transfer tool (ratt) [14] for transferring annotations between species., using ratt [14] synteny between the reference and the query, […]

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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