Under both BP and MF GO aspects and both alignments, we observe a consistent trend in the quality of the solutions produced by the different aligners. IsoRank produces alignments of reasonable biological, but poor topological quality, whereas MI-GRAAL exhibits the opposite behavior (i.e. high topological, but poor biological quality). Natalie 2.0 and GHOST consistently produce alignments with competitive trade offs between the competing goals of topological and biological quality, though GHOST’s alignments exhibit consistently higher topological quality