use PDL;

# amino acids in this order in the reaction rates pdl
# A R N D C Q E G H I L K M F P S T W Y V B Z X
$rates = pdl [
    [ 5, -2, -1 ],
    [ -2, 7, -1 ],
    [ -1, -1, 7 ],
];

$multiplied_rates = $rates x $rates;
print $multiplied_rates;