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.

Downloading Mauve

Mauve is distributed free-of-charge for Windows, Mac OS X, and Linux.  Please visit the download section to obtain a copy of Mauve. 

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

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 free-access (but not open-access! )  from the Genome Research website.

Screenshots of Mauve

These are screenshots of Mauve 2.0 visualizing an alignment of nine Yersinia genomes: