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. Mauve 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.

What's New in This Release: [ read full changelog ]

Major new features:
· Reordering contigs of draft genomes, published as Rissman et al 2009
· Export a list of Single Nucleotide Polymorphisms present in an alignment (thanks to Meg Woolfit for the suggestion)
· Export a file listing the genome arrangement as a signed permutation
· Export a list of positionally orthologous CDS, tRNAs, or misc_RNAs (thanks to Elizabeth Skippington for the suggestion)
· Export a file containing alignments of orthologous CDS, including alignments of unannotated regions predicted to be orthologous (thanks to Sam Sheppard for the idea)

Other new features::
· On Linux it is now possible to launch Mauve from outside the Mauve directory (thx Dongying Wu)
· Option to disable drawing the mouse cursor highlighting orthologous regions so that figures for manuscripts can be rendered (thanks to Andrew Kropinski for the idea)

Bugs fixed:
· An alignment would complete successfully but the viewer would fail to load it because the alignment contained invalid data in the backbone file. This bug was very commonly encountered in 2.2.0.
· An alignment with progressiveMauve would crash with an error like "cga doesn't fit" or another error message, when run on multicore computers. This was a race condition in progressiveMauve's parallelism.

Known issues:
· Parallelism has been disabled for all supported platforms to avoid a race condition bug.