Comparison of the quality of T alignments versus the corresponding T+S alignments, under each of the PE and ME frameworks. Each bar shows the number of cases (here, a case refers to a combination of NA method, a network pair/set, and an alignment quality measure) in which the T alignment is superior, the T+S alignment is superior, or the two alignments are tied (i.e., within 1% of each other’s accuracy). The cases are separated into network pairs/sets with known true node mapping and network pairs/sets with unknown true node mapping.