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Mauve specifications


Unique identifier OMICS_00940
Name Mauve
Alternative name progressiveMauve
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Output data An alignment file, an orthologs file, an SNP file, a LCB boundary file, a permutation matrix file, an identity matrix file, a guide tree file, a file with regions of the alignment sequence where sequences is conserved among all of the genomes being aligned, and an islands file.
Output format XMFA+NEWICK+TSV
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 2.4.0
Stability Stable
Maintained Yes




No version available


  • person_outline Aaron E. Darling

Additional information

Publications for Mauve

Mauve citations


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

[…] followed by Sanger sequencing. The annotated plastid genomes were visualized using OrganellarGenomeDraw v1.2 []. Comparative analysis of the genome structure was accomplished using UniMoG v1.0 [] and Mauve Genome Alignment v2.2.0 [, ] through the Geneious plug-in using the default setting []. […]


Comparative genomic analysis of multidrug resistant Streptococcus pneumoniae isolates

PMCID: 5939923
PMID: 29765237
DOI: 10.2147/IDR.S147858

[…] ). Gaps inside the scaffold were closed with GapCloser (version 1.12) ( All newly sequenced genomes were ordered on the basis of the reference genome with Mauve (version 2.3.1). For each genome, regions that were absent in the reference genome were extracted with custom Perl script, and were then searched against the SwissProt database using blastx (ver […]


Comparative genomics of cocci shaped Sporosarcina strains with diverse spatial isolation

BMC Genomics
PMCID: 5930826
PMID: 29716534
DOI: 10.1186/s12864-018-4635-8

[…] Contigs for each of the draft genomes (Illumina sequenced strains and S. ureae str. DSM 2281) were re-ordered using the program Mauve (v2.4.0) [], with the closest related strain with a complete genome utilized as the reference genome. Next, Artemis Comparison Tool (ACT) comparison files were generated between two targeted gen […]


The reporting of a Bacillus anthracis B clade strain in South Africa after more than 20 years

BMC Res Notes
PMCID: 5930959
PMID: 29716659
DOI: 10.1186/s13104-018-3366-x
call_split See protocol

[…] CLC Genomics Workbench version 7.5 (CLC, Denmark). The assembled contigs were aligned with BLASTn [] using B. anthracis Ames ancestor (GenBank: AE017334.2, AE017336.2, and AE017336.2) as a reference. Mauve tool [] was used to align and order the assembled contigs using B. anthracis Ames ancestor as a reference. The genome was annotated using PGAAP at NCBI [].The trimmed reads of B. anthracis KC201 […]


Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans

Nat Commun
PMCID: 5931558
PMID: 29717136
DOI: 10.1038/s41467-018-03857-x

[…] ad. If a reference locus was not sufficiently covered, the character “N” was inserted at the respective position.A multiple genome alignment of 33 M. leprae genomes was computed using the progressive Mauve algorithm integrated in the whole genome alignment software Mauve v2.4.0. The sequences of the ten medieval genomes G34, G154, G404, G427, G507, G533, G722, G749, G1083, and G1149, five previous […]


Analysis of Theileria orientalis draft genome sequences reveals potential species level divergence of the Ikeda, Chitose and Buffeli genotypes

BMC Genomics
PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2

[…] e A5-miseq (v2015–05-22) pipeline []. Levels of remaining host DNA were assessed and filtered using BioBloomTools [] and the B. taurus genome sequence []. Whole genome alignments were performed using progressiveMauve from Mauve v2.4.0 and nucmer from MUMmer v3.23 [, ]. For analysis of gene presence/absence, genes were annotated using Maker v3.00 beta [] to combine the annotation tracks derived fro […]


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Mauve institution(s)
Genome Center and Department of Computer Science, University of Wisconsin, Madison, WI, USA; Biotechnology Center and Department of Oncology, University of Wisconsin, Madison, WI, USA; Genome Center and Department of Genetics, University of Wisconsin, Madison, WI, USA
Mauve funding source(s)
Supported in part by National Institutes of Health (NIH) grant R01-GM62994 and National Science Foundation (NSF) grant DBI0630765, and in part, with federal funds from the National Institute of Allergy and Infectious Diseases, NIH, Department of Health and Human Services, under Contract No. HHSN266200400040C.

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