There is no monolithic program, wurst. Instead, this is a framework which works mostly with proteins and lets one do things like sequence to structure alignments, sequence alignments and pure structural alignments.
The philosophy is that there is a set of low level routines coded in C. These are called from perl. To do anything useful, you write a little perl script which calls the functions you want.
Scripts have been written to do things such as parameter optimization using a simplex or protein structure-based phylogeny using a guide tree-based method.
or, depending on the directory you are running from,
use lib "$FindBin::Bin/../src/Wurst/blib/arch";
use lib "$FindBin::Bin/../src/Wurst/blib/lib";