▁twice ▁that ▁which ▁separ ates ▁them ▁from ▁their ▁common ▁ancest or . ▁If ▁a ▁range ▁of ▁P AM ▁matrices ▁are ▁used ▁to ▁align ▁two ▁prote ins ▁that ▁are ▁known ▁to ▁be ▁related , ▁then ▁the ▁value ▁of ▁ ▁in ▁the ▁P AM n ▁matrix ▁which ▁results ▁in ▁the ▁best ▁score ▁is ▁most ▁likely ▁to ▁correspond ▁to ▁the ▁mut ations ▁per ▁am ino ▁acid ▁separ ating ▁the ▁two ▁prote ins . ▁Hal ving ▁this ▁value ▁and ▁div iding ▁by ▁the ▁rate ▁at ▁which ▁accepted ▁mut ations ▁accum ulate ▁in ▁the ▁protein ▁family ▁provides ▁an ▁estimate ▁of ▁the ▁time ▁of ▁diver gence ▁of ▁these ▁two ▁prote ins ▁from ▁their ▁common ▁ancest or . ▁That ▁is , ▁the ▁time ▁of ▁diver gence ▁in ▁my r ▁is ▁ ▁Where ▁ ▁is ▁the ▁number ▁of ▁mut ations ▁per ▁am ino ▁acid , ▁and ▁ ▁is ▁the ▁rate ▁of ▁accepted ▁mut ation ▁accum ulation ▁in ▁mut ations ▁per ▁am ino ▁acid ▁site ▁per ▁million ▁years . ▁ ▁Use ▁in ▁B LA ST ▁P AM ▁matrices ▁are ▁also ▁used ▁as ▁a ▁scoring ▁matrix ▁when ▁comparing ▁DNA ▁sequences ▁or ▁protein ▁sequences ▁to ▁judge ▁the ▁quality ▁of ▁the ▁alignment . ▁This ▁form ▁of ▁scoring ▁system ▁is ▁util ized ▁by ▁a ▁wide ▁range ▁of ▁alignment ▁software ▁including ▁B LA ST . ▁ ▁Compar ing ▁P AM ▁and ▁B L OS UM ▁In ▁addition ▁to ▁P AM ▁matrices , ▁another ▁more ▁recently ▁developed ▁scoring ▁matrix ▁can ▁be ▁used . ▁This ▁is ▁known ▁as ▁a ▁B L OS UM . ▁The ▁two ▁result ▁in ▁the