Mauve protocols

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Mauve computational protocol

Mauve specifications

Information


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

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Maintainer


  • person_outline Aaron E. Darling <>

Additional information


http://darlinglab.org/mauve/user-guide/introduction.html

Publications for Mauve

Mauve IN pipelines

 (118)
2018
PMCID: 5794934
PMID: 29437087
DOI: 10.1128/genomeA.01223-17

[…] using velvet 1.2.10 set at default for all parameters (9). contigs were organized by aligning to the genome sequence of the reference strain s. typhimurium lt2 (accession no. nc_003197) using mauve multiple alignments (10). whole-genome multilocus sequence typing was performed using enterobase (https://enterobase.warwick.ac.uk/). a total of three sequence types, st19 (n = 9), st1695 (n = […]

2018
PMCID: 5807335
PMID: 29459888
DOI: 10.3389/fcimb.2018.00020

[…] 36, 33, and 3.5 kb in contig_1, contig_2, and contig_3, respectively and each have a gc content of between 35.3 and 37.1%. most likely contig_2 and contig_3 are part of the same phage according to a mauve comparison (darling et al., 2004; data not shown). therefore, the phages identified in jf5203 have approximately the same size as those previously reported for this cluster, as well […]

2018
PMCID: 5821093
PMID: 29440577
DOI: 10.1128/mBio.02381-17

[…] ltd., auckland, new zealand). sequence features were annotated using the geneious 8 annotation transfer tool, and sequences were aligned using a combination of blast (29), muscle (30), progressive mauve (31), and lastz alignment tools. average nucleotide identity data were calculated using blast (anib) and jspecies (32), core genome alignments were performed using panseq (33), and phylogenetic […]

2018
PMCID: 5826093
PMID: 29511354
DOI: 10.1177/1176934318759299

[…] with other commonly used and several innovative phylogenetic approaches such as the super-matrix concatenation of alignments of orthologous gene sequences, 16s ribosomal rna (rrna) phylogenetics, mauve whole genome alignment,28 and cvtree oligopeptide profiling.29 sequenced strains of prochlorococcus marinus, of which phylogenetic relations have been discussed before,30 were used as a case […]

2018
PMCID: 5834334
PMID: 29496837
DOI: 10.1128/genomeA.00119-18

[…] 10.1.3 (9), followed by repeat spanning and gap closure with sanger sequencing of pcr products. the complete genome was compared to that of s. uberis 0104j (genbank accession number am946015) by progressivemauve alignment (10). genomic features and coding dna sequences (cdss) were predicted with the ncbi prokaryote genome annotation pipeline (pgap) (11)., the complete nz01 genome comprises […]

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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