of substitutions is not affected by the position of the root.  Rule 1.  When the two descendent nodes of an ancestral node have some states (nucleotides or amino acids) in common, the ancestral node is assigned to the set of common states.  In this case, the most parsimonious explanation does not require any substitutions.  Rule 2.  When the two descendant nodes have no states in common, then all states in the descendent nodes are combined to form the set of possible states at the ancestral node.  In this c