Maybe something like this? Assumes symmetry (d(x, y) = d(y, x)).

my @sim;
my @words = ...;

for my $i (0 .. $#words) {
    for my $j ( ($i+1) .. $#words) {
        $sim[$i][$j] = similarity( $words[$i], $words[$j])
        $sim[$j][$i] = $sim[$i][$j];
    } 
}

sub similarity {
   my ( $w1, $w2 ) = @_;
   my $sim = 1;
   # calc simularity
   return sim;
}
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