Are you looking for something like this?

use warnings;
use strict;

my $word = qr/(?<!\p{Alnum})\p{Alnum}+(?!\p{Alnum})/;
my %count;
my $counter;

while (my $line = <DATA>) {
    while ($line =~ /($word('$word)?)/g){
        $count{$1}++;
    }
}

 for (sort {$count{$b} <=> $count{$a} || lc $a cmp lc $b } keys %count
+)
{
  printf "%15s %5d\n", $_, $count{$_};
  last if ++$counter > 100;
};

__DATA__
"Hello World!"
"Oh poor Yorick, his world I knew well yes I did"
"don't won't, can't shouldn't, you'll, it's, etc."
"Señor Montóya's resüme isn't ápropos."
the, the, the, the, the, the, the, the, the, the

[download]

It isn't very clear what you mean by "words-by-words matrix".

In reply to Re: a question about making a word frequency matrix by thundergnat
in thread a question about making a word frequency matrix by peacekorea

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.