Mixing the two is not probably something you should do. Yes, PHP is weak when it comes to manipulating nested data structures, however the difficulty and general messiness of adding Perl to your PHP makes that approach rather abortive. I'd personally either keep the two separate and use an AJAX (Javascript) pull from your Perl script to populate data on your PHP page, or do the page entirely in Perl. Or depending on your needs, you could substitute a properly-designed MySQL query for data manipulation in either language. What precisely are you trying to do?
I use both Perl and PHP for work, incidently - Perl for complicated data processing and PHP for more presentation-oriented sites. I try not to mix the two much in the same site, though.
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