▁basis ▁of ▁having ▁high ▁similarity ▁with ▁their ▁prede cess ors . ▁The ▁protein ▁align ments ▁included ▁were ▁required ▁to ▁display ▁at ▁least ▁ 8 5 % ▁identity . ▁As ▁a ▁result , ▁it ▁is ▁reasonable ▁to ▁assume ▁that ▁any ▁aligned ▁mismatch es ▁were ▁the ▁result ▁of ▁a ▁single ▁mut ation ▁event , ▁rather ▁than ▁several ▁at ▁the ▁same ▁location . ▁ ▁Each ▁P AM ▁matrix ▁has ▁twenty ▁rows ▁and ▁twenty ▁columns ▁— ▁one ▁representing ▁each ▁of ▁the ▁twenty ▁am ino ▁ac ids ▁translated ▁by ▁the ▁gen etic ▁code . ▁The ▁value ▁in ▁each ▁cell ▁of ▁a ▁P AM ▁matrix ▁is ▁related ▁to ▁the ▁probability ▁of ▁a ▁row ▁am ino ▁acid ▁before ▁the ▁mut ation ▁being ▁aligned ▁with ▁a ▁column ▁am ino ▁acid ▁afterwards . ▁From ▁this ▁definition , ▁P AM ▁matrices ▁are ▁an ▁example ▁of ▁a ▁substitution ▁matrix . ▁ ▁Collection ▁of ▁data ▁from ▁ph y log en etic ▁trees ▁For ▁each ▁branch ▁in ▁the ▁ph y log en etic ▁trees ▁of ▁the ▁protein ▁families , ▁the ▁number ▁of ▁mismatch es ▁that ▁were ▁observed ▁were ▁recorded ▁and ▁a ▁record ▁kept ▁of ▁the ▁two ▁am ino ▁ac ids ▁involved . ▁These ▁counts ▁were ▁used ▁as ▁entries ▁below ▁the ▁main ▁diagonal ▁of ▁the ▁matrix ▁. ▁Since ▁the ▁vast ▁majority ▁of ▁protein ▁samples ▁come ▁from ▁organ isms ▁that ▁are ▁alive ▁today ▁( ext ant ▁species ), ▁the ▁' direction ' ▁of ▁a ▁mut ation ▁cannot ▁be ▁determined . ▁That ▁is , ▁the ▁am ino ▁acid ▁present ▁before ▁the ▁mut ation ▁cannot ▁be ▁distinguished ▁from ▁the ▁am