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About Mauve Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics. Aligning whole genomes is a fundamentally different problem than aligning short sequences. Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. Mauve is distributed free-of-charge for Windows, Mac OS X, and Linux. Please visit the download section to obtain a copy of Mauve. After installing Mauve, we suggest subscribing to the mauve-announce and mauve-users mailing lists. The mauve-announce mailing list is a low-traffic list on which we make announcements about new software versions with bug fixes and new features. The mauve-users list is a general discussion forum for users of the Mauve software to communicate with each other and resolve usage issues. Prior to posting a usage-related question about Mauve to the mauve-users list, please search the mauve-users list archives Other software based on Mauve Various analysis tools have been developed to make inference on the basis of Mauve genome alignments. We maintain a listing of Mauve-based tools. Citing Mauve in a Publication If you use the progressiveMauve algorithm, please cite: Aaron E. Darling, Bob Mau, and Nicole T. Perna. 2010. progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss, and Rearrangement. PLoS One. 5(6):e11147.
The original Mauve paper was published as: Aaron C.E. Darling, Bob Mau, Frederick R. Blatter, and Nicole T. Perna. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Research. 14(7):1394-1403.
The paper is now freely available from the Genome Research website.
Screenshots of Mauve These are screenshots of Mauve 2.0 visualizing an alignment of nine Yersinia genomes:  
 
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