use strict;
use warnings;

my $sites = [
    'CGGCGGAAAACTGTCCTCCGTGC',    # mouse
    'CGACGGAACATTCTCCTCCGCGC',    # rat
    'CGACGGAATATTCCCCTCCGTGC',    # human
    'CGACGGAAGACTCTCCTCCGTGC',    # chimp
    ];

my @val = my_parsimony ($sites);
print @val;


sub my_parsimony {
    my ($sites) = @_;
    my $lastSite = $sites->[0];
    my @mincol = (0) x length $lastSite;

    for my $nextSite (@$sites) {
        my $changes = $lastSite ^ $nextSite;
        
        $lastSite = $nextSite;
        next unless $changes =~ s/[^\0]/+/g;

        my $pos = 0;

        ++$mincol[$pos++] while -1 != ($pos = index $changes, '+', $pos);
    }

    return @mincol;
}

##</code><code>##

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