You're wondering if there is a package that automatically generates PRMT values?

I am unaware of a pre-packaged point and click utility, but it's a pretty straightforward process (see Larsen et al 2011) for metagenomic data. I was able to calculate PRMT values for soil microbial transcripts pretty quickly after reading that paper. You can quickly do this in the bash shell, with AWK/SED, in Python/Perl/R, or (gasp) Excel (or some other spread sheet program).