"it sounds like you've made this problem overly complex" I probably have, but this is the result of reading tutorials on the web... everyone seems to assume that I want to install CPAN packages... 
 
Here is the download link: http://www.mybiosoftware.com/protein-sequence-analysis/11826 
 
Beware, someone in my institute who knows a bit of Perl told me it is not the most elegantly written script he has ever seen...

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.

Arthfael:

Ugh! It looks like someone round-tripped the McCarthy-SourceData.txt file through Excel. The ninth column looks as if it's been munged (12/18 being turned into 18-Dec, etc.).

...roboticus

When your only tool is a hammer, all problems look like your thumb.