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 on a new scale. 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.

Whats New in This Release:

New features:
· Display each component of multi-part features (e.g. a multiple exon gene) as a linked series of boxes
· Display repeat_region annotations from GenBank files
· Improved load time for previously viewed alignments using a disk-based alignment cache
· Added a help menu item that will clear the on-disk alignment cache
· Colorized the similarity plots, grey was starting to depress our entire lab.
· Support for highlighting arbitrary regions of the sequence by holding the shift key while clicking and dragging on the display
· Faster nucleotide display when zoomed in closely

Bug fixes:
· Fixed GUI interface for setting the minimum seed size (Thanks to Bill Bruno and Todd Treangen)
· Fixed mouseover, highlighting, and display alignment in the LCB display mode (used when the Full Alignment option is disabled).