This script requires the BioPerl suite of modules. I'm running Strawberry Perl 5.18.2 on Windows 7 64bit, DWIM perl ships with Strawberry 5.14, which isn't anything to worry about. To install BioPerl open a command prompt and type the following:

cpan BioPerl
[download]

This will download, unpack and build the distribution and it's dependencies automatically. This may take some time. I skipped the online tests (they'd fail from my work laptop due to network issues). After this you can run the software you linked to by unpacking the download and just running the script:

C:\datasetConstructor>perl pepFly.pl
Input File>
# of output files>
[download]

Let me know if you have any problems. Note that I'm not a Bioinformatician. See also Tutorials->Perl and Bioinformatics.

Update: fixed typo.