Added lines for NUCmer compatibility

LASTZ alignment was not working for me, so I added some lines to use NUCmer for alignment instead.  Because NUCmer produces alignments in "delta" format, I had to use two different tools from two different packages (mugsy "delta2maf" and lastz "maf-convert") to perform conversion.  I'm not sure whether you can package those two scripts directly with COMPASS based on their licenses, but that would probably be easiest if it is the case.