To install the modified version of each software, follow the original guideline
for each software.  Only the version with default parameters was tested for
each software.

To change the parameters omega and beta in nralign, find all comments
/* nralign */ within the source codes.  Note that there are two places that
need to be changed in MUMMALS.

More information is available at http://faculty.cs.tamu.edu/shsze/nralign.