A few weeks ago, on December 22, 2011 actually, I released a new filter for adding Perl support to Doxygen. This filter supports Doxygen style comments, POD style comments, and can perform some basic analysis of a Perl module and is called Doxygen::Filter::Perl. You can download this filter from CPAN or from Sourceforge at: http://perldoxygen.sourceforge.net/. For windows users or first time Doxygen users, please see the discussion thread on the Sourceforge project page. For those familiar with Doxygen, the documentation on CPAN should suffice.
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