My most revered monks,

The subroutine below compute the number of mismatches between two strings (they are always equal) - usually called Hamming Distance.

However my code below is painfully slow. I am terribly in need of a super fast way to do this. In particular it has to process millions of string pairs.

Thus I turn to you my brother monks, for illumination in this matter.

#!/usr/bin/perl -w
use strict;

my $s1 = 'AAAAA';
my $s2 = 'ATCAA';
my $s3 = 'AAAAA';

hd($s1,s2) # will give value 2
hd($s1,s3) # will give value 0

sub hd
{
     #String length is assumed to be equal
     my ($k,$l) = @_;
     my $len = length ($k);
     my $num_mismatch = 0;

     for (my $i=0; $i<$len; $i++)
     {
      ++$num_mismatch if substr($k, $i, 1) ne substr($l, $i, 1);
     }

     return $num_mismatch;
}
[download]

Update: Benchmark. Thanks so much everybody.

          Rate  Mine    RJ   BWK inman
Mine  176987/s    --  -65%  -78%  -80%
RJ    504123/s  185%    --  -38%  -44%
BWK   817943/s  362%   62%    --   -9%
inman 901871/s  410%   79%   10%    --

*Note: Mine has already included the modification
suggested by 'wazoox'.
[download]