▁used ▁more ▁regularly . ▁Because ▁the ▁value ▁ ▁in ▁the ▁P AM n ▁matrix ▁represents ▁the ▁number ▁of ▁mut ations ▁per ▁ 1 0 0 ▁am ino ▁ac ids , ▁which ▁can ▁be ▁li ken ed ▁to ▁a ▁percentage ▁of ▁mut ations , ▁the ▁term ▁percentage ▁accepted ▁mut ation ▁is ▁sometimes ▁used . ▁ ▁It ▁is ▁important ▁to ▁distinguish ▁between ▁point ▁accepted ▁mut ations ▁( P AM s ), ▁point ▁accepted ▁mut ation ▁matrices ▁( P AM ▁matrices ) ▁and ▁the ▁P AM n ▁matrix . ▁The ▁term ▁' point ▁accepted ▁mut ation ' ▁refers ▁to ▁the ▁mut ation ▁event ▁itself . ▁However , ▁' P AM ▁matrix ' ▁refers ▁to ▁one ▁of ▁a ▁family ▁of ▁matrices ▁which ▁contain ▁scores ▁representing ▁the ▁lik elihood ▁of ▁two ▁am ino ▁ac ids ▁being ▁aligned ▁due ▁to ▁a ▁series ▁of ▁mut ation ▁events , ▁rather ▁than ▁due ▁to ▁random ▁chance . ▁The ▁' P AM n ▁matrix ' ▁is ▁the ▁P AM ▁matrix ▁corresponding ▁to ▁a ▁time ▁frame ▁long ▁enough ▁for ▁ ▁mut ation ▁events ▁to ▁occur ▁per ▁ 1 0 0 ▁am ino ▁ac ids . ▁ ▁Const ruction ▁of ▁P AM ▁matrices ▁ ▁P AM ▁matrices ▁were ▁introduced ▁by ▁Margaret ▁Day hoff ▁in ▁ 1 9 7 8 . ▁The ▁calculation ▁of ▁these ▁matrices ▁were ▁based ▁on ▁ 1 5 7 2 ▁observed ▁mut ations ▁in ▁the ▁ph y log en etic ▁trees ▁of ▁ 7 1 ▁families ▁of ▁closely ▁related ▁prote ins . ▁The ▁prote ins ▁to ▁be ▁studied ▁were ▁selected ▁on ▁the