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.
Citation requested if the progressiveMauve feature is used: 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.
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