|Mauve: multiple, similar genome alignments with rearrangement|
Mauve has the ability to align multiple genomes, in spite of the presence of rearrangements and inversions, as long as they are quite similar. It is not nearly as fast as MUMmer, but is more appropriate in some instances.
Using Mauve on HPC
Mauve can be driven through an X11 Java interface or through a command line executable. Documentation is available online. Mauve is able to align rearranged genomes using an anchored locally collinear blocks (LCBs) approach. The Java GUI is launced with the "Mauve" command, and the command line interface is launched with the command "mauveAligner." Be sure that you are conneced to HPC with an X tunnelled ssh session if you want to use the Java GUI.