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.
The new release fixes a missing library problem on Mac OS X. Other fixes include reduced memory usage in some cases, a fix for the failure of the sequence navigator to highlight annotation search results, and a divide-by-zero that rarely arose in progressiveMauve.
URL: Genome Evolution Laboratory - Mauve Genome Alignment Software