Other differences between Aligator and BracketMaker rankings are related to the number of A sites used and their relative placement to C sites. Every A ligation is given a -2 score penalty in Aligator, but in BracketMaker, multiple adjacent A sites result in only +1 additional path length from the combined desulfurization step regardless of their number. The differences between Aligator and BracketMaker scores highlight the need for a nuanced analysis of synthesis plans and human interpretation of the output scores.