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. License: GNU General Public License (GPL) Changes: This release includes alignment accuracy improvements, visualization improvements, and numerous bugfixes. The alignment algorithm has been parallelized to run on multi-core CPUs, and 64-bit builds are included. The user's guide has been rewritten to include Progressive Mauve.

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