John - you can run Perl scripts via the perl function. From this link,
perl('perlfile') calls the Perl script perlfile, using the appropriate operating system Perl executable. Perl is included with the MATLAB® software on Microsoft® Windows® systems, and thus MATLAB users can run user-created MATLAB functions containing the perl function. On Linux® and Macintosh systems, MATLAB calls the Perl interpreter available with the operating system.