Jarkko Hietaniemi used http://pmd.sourceforge.net/cpd.html to do duplicate code detection against the Perl source code, but I'm not sure that this tool will work well with Perl as it does a lot of parsing. Google found me another paper on lightweight detection of duplicated code, which sounds easy to implement and use with Perl. The trick in the paper seems to be to use a sliding window over sections of code and then to do a bag comparison, to protect against swapped lines etc.