▁nor ▁are ▁mut ations ▁which ▁are ▁le th al ▁or ▁which ▁are ▁rejected ▁by ▁natural ▁selection ▁in ▁other ▁ways . ▁ ▁A ▁P AM ▁matrix ▁is ▁a ▁matrix ▁where ▁each ▁column ▁and ▁row ▁represents ▁one ▁of ▁the ▁twenty ▁standard ▁am ino ▁ac ids . ▁In ▁bio in format ics , ▁P AM ▁matrices ▁are ▁regularly ▁used ▁as ▁substitution ▁matrices ▁to ▁score ▁sequence ▁align ments ▁for ▁prote ins . ▁Each ▁entry ▁in ▁a ▁P AM ▁matrix ▁indicates ▁the ▁lik elihood ▁of ▁the ▁am ino ▁acid ▁of ▁that ▁row ▁being ▁replaced ▁with ▁the ▁am ino ▁acid ▁of ▁that ▁column ▁through ▁a ▁series ▁of ▁one ▁or ▁more ▁point ▁accepted ▁mut ations ▁during ▁a ▁specified ▁evolution ary ▁interval , ▁rather ▁than ▁these ▁two ▁am ino ▁ac ids ▁being ▁aligned ▁due ▁to ▁chance . ▁D ifferent ▁P AM ▁matrices ▁correspond ▁to ▁different ▁lengths ▁of ▁time ▁in ▁the ▁evolution ▁of ▁the ▁protein ▁sequence . ▁ ▁Bi ological ▁background ▁The ▁gen etic ▁instructions ▁of ▁every ▁rep lic ating ▁cell ▁in ▁a ▁living ▁organ ism ▁are ▁contained ▁within ▁its ▁DNA . ▁Through out ▁the ▁cell ' s ▁lifetime , ▁this ▁information ▁is ▁trans cribed ▁and ▁rep licated ▁by ▁cell ular ▁mechan isms ▁to ▁produce ▁prote ins ▁or ▁to ▁provide ▁instructions ▁for ▁daughter ▁cells ▁during ▁cell ▁division , ▁and ▁the ▁possibility ▁exists ▁that ▁the ▁DNA ▁may ▁be ▁alter ed ▁during ▁these ▁processes . ▁This ▁is ▁known ▁as ▁a ▁mut ation . ▁At ▁the ▁mole cular ▁level , ▁there ▁are ▁regul atory ▁systems ▁that ▁correct ▁most ▁— ▁but ▁not ▁all ▁— ▁of ▁these