Mauve constructs global multiple alignments of
rearranged genome sequences. It also provides an
interactive display of multi-species sequence
conservation and any annotated features in those
genomes. It can be applied for sequence comparison of both finished or incomplete genomes in multiple contigs. The
resulting display is useful for identifying
functional chromosomal regions under selective
pressure and for performing ortholog assignment
based on conserved gene order. Mauve writes global
alignments in eXtended Multi-FastA (XMFA) format,
a phylogenetic guide tree in Newick format, and
the location of genomic islands. It identifies the
breakpoints of genomic rearrangement and can
provide a reduction of the genomes to a signed
permutation matrix suitable for inference of
rearrangement history.
