What I would do is take each word, split up the letters, and sort them alphabetically. Then you have a hash key which will be the same for "top", "pot", and so on. Here is an example.

use strict;
use Data::Dumper;
my @words = qw/opt top pot pit tip/;
my %count;
foreach my $w(@words) { 
    my $key = join '', sort split '', $w;
    $count{$key}++;
}

print Dumper \%count;
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Output:

$VAR1 = {
          'opt' => 3,
          'ipt' => 2
        };
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Update: Added the D::D output.