Doesn't BioPerl already do this stuff? Regardless, you should die if the user doesn't give you what you want. Then, you can split each seq into characters and loop over them:

use warnings;
use strict;

die "provide two sequences \n" unless @ARGV == 2;
die "ensure the sequences are the same length \n" unless length($ARGV[
+0]) == length($ARGV[1]);

my @s1 = split //, $ARGV[0];
my @s2 = split //, $ARGV[1];
my $cnt = 0;
for my $i (0 .. $#s1) {
    if ($s1[$i] ne $s2[$i]) {
        printf "pos %d: %s => %s\n", $i+1, $s1[$i], $s2[$i];
        $cnt++;
    }
}
print "snps = $cnt\n";
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