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MAUVE GENOME ALIGNMENT

Easily align and compare conserved regions across multiple genomes using the Mauve alignment algorithm. PRICING DOWNLOAD FREE TRIAL

Use MegAlign Pro to easily perform a Mauve genome alignment and compare multiple genomes with structural complexity.

In the realm of multiple sequence aligners, the trusted Mauve algorithm stands apart from its traditional counterparts through its ability to align chromosome length sequences and sequences that contain structural rearrangements. Multiple genome alignments often require methods separate from traditional multiple sequence aligners, requiring you to go between various tools for your analysis. That’s why we’ve seamlessly integrated the Mauve algorithm into MegAlign Pro, so that everything you need for all of your multiple sequence alignments is in one easy-to-use application. Simply drag and drop your genomes into MegAlign Pro and perform a Mauve genome alignment using the default settings, or modify parameters to meet your needs. Following the genome alignment, MegAlign Pro makes it easy to navigate to and view conserved regions across multiple sequences, even at various zoom levels. Customize the appearance of your alignment as desired before exporting a publication-quality, editable image. Use MegAlign Pro to easily perform Mauve genome alignments in the same application you trust for all your multiple sequence alignment needs.

Mauve genome alignment in 4 simple steps

Mauve Genome Alignment Step 1

Step 1

Add genome sequences

Mauve Genome Alignment Step 2

Step 2

Perform alignment using Mauve method

Mauve Genome Alignment Step 3

Step 3

View and analyze results in multiple views

Mauve Genome Alignment Step 4

Step 4

Customize appearance and export for publication

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Learn more about Mauve genome alignment

Resources | Tutorials | FAQs | Citations | User Guide

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Resources

Please see our resources below for more information on Mauve genome alignment.

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Aligning and Annotating Multiple Genomes Webinar

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Best Practices for Sequence Alignment in MegAlign Pro Webinar

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Answers to Your MegAlign Pro Webinar Questions

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Tree Viewer Software

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Tutorials

Watch one of our videos or check out one of our written tutorials to learn more about using MegAlign Pro for Muave genome alignments and other multiple sequence alignments.

Phylogenetic Trees in MegAlign Pro

See how to easily generate and customize phylogenetic trees in MegAlign Pro to predict evolutionary relationships.

Merging and Realigning Sequences in MegAlign Pro

In this video, learn how to perform profile alignments to merge two alignments together. In addition, learn how to merge and realign additional sequences in your MegAlign Pro project.

Aligning Multi-Segment Files

In this video, learn how to work with multi-segment files in MegAlign Pro. Multi-segment files are files that consist of more than one chromosome, contig, or fragment, and must be aligned end to end before conducting multiple sequence alignments.

FAQs

What file types can I use for a Mauve genome alignment in MegAlign Pro?

MegAlign Pro can align any sequence file in GenBank, FASTA, or DNA Multi-seq format, as well as any sequence file saved from a Lasergene application.

Can I modify my Mauve genome alignment?

Yes. Following your Mauve genome alignment, you may choose to realign a range of aligned sequences in the active block using different parameters or a different alignment engine, or realign existing aligned sequences plus additional unaligned sequences.

What’s the easiest way to find sequence matches for my consensus sequence?

MegAlign Pro’s Search wizard, accessed using Search > Sequence Search, lets you search a query sequence against one of NCBI’s BLAST databases. The sequence can be part or all of an active sequence, another sequence file on your computer, or typed/pasted-in text.

Can I export my phylogenetic tree following a Mauve genome alignment?

Yes. Select File > Export Data > Tree to export your phylogenetic tree in either Newick or Nexus formats, which are compatible with third part tree editing programs like FigTree.

You can also specify the third party tree viewer you use under Edit>Preferences to gain the ability to open your phylogenetic tree directly in that tree viewer by selecting File>Send Tree to Tree Viewer.

How do I export an image of my Mauve genome alignment?

To export an image of your Mauve genome alignment, choose File > Export Image > (View Name) and choose the export format: Adobe PDF (.pdf), Microsoft PowerPoint-optimized (.pptx), PNG image (.png) or JPG image (.jpg, .jpeg).

Citations

Prevalence of Shiga toxin-producing Shigella species isolated from French travellers returning from the Caribbean: an emerging pathogen with international implications
M.D. Gray, D.W. Lacher, S.R. Leonard, J. Abbott, S. Zhao, K.A. Lampel, E. Prothery, M. Gouali, F.-X. Weill, A.T. Maurelli. Clinical Microbiology and Infection, Volume 21, Issue 8, 2015, Pages 765.e9-765.e14, ISSN 1198-743X.

Complete-genome sequencing elucidates outbreak dynamics of CA-MRSA USA300 (ST8-spa t008) in an academic hospital of Paramaribo, Republic of Suriname.
Sabat, A., Hermelijn, S., Akkerboom, V. et al.  Sci Rep 7, 41050 (2017).

Internal sample process control improves cultivation-independent quantification of thermotolerant Campylobacter.
Pacholewicz, Ewa, Buhler, Christiane, Wulsten, Imke F., Kraushaar, Britta, Luu, Huong Quynh, Iwobi, Azuka N., Huber, Ingrid, Stingl, Kerstin. Food Microbiology, Volume 78, 2019, Pages 53-61, ISSN 0740-0020.

Genome alterations associated with improved transformation efficiency in Lactobacillus reuteri.
Ortiz-Velez, L., Ortiz-Villalobos, J., Schulman, A. et al. Microb Cell Fact 17, 138 (2018).

New insights into the role of plasmids from probiotic Lactobacillus pentosus MP-10 in Aloreña table olive brine fermentation.
Abriouel, H., Pérez Montoro, B., de la Fuente Ordoñez, J.J. et al. Sci Rep 9, 10938 (2019).

A Strain of an Emerging Indian Xanthomonas oryzae pv. oryzae Pathotype Defeats the Rice Bacterial Blight Resistance Gene xa13 Without Inducing a Clade III SWEET Gene and Is Nearly Identical to a Recent Thai Isolate.
Carpenter SCD, Mishra P, Ghoshal C, Dash PK, Wang L, Midha S, Laha GS, Lore JS, Kositratana W, Singh NK, Singh K, Patil PB, Oliva R, Patarapuwadol S, Bogdanove AJ and Rai R. Front. Microbiol. 9:2703 (2018).

Evolutionarily conserved partial gene duplication in the Triticeae tribe of grasses confers pathogen resistance.
Rajaraman, J., Douchkov, D., Lück, S. et al. Genome Biol 19, 116 (2018).

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    Carl Lawyer, M.D.

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    Rui Jin, Emory University

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    “The most comprehensive and full-featured alignment software I have found.”

    Gordon Wolfe, California State University Chico

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