There recently has been great interest in aligning protein-protein interaction (PPI) networks to identify potentially orthologous proteins between species. It is thought that the topological information contained in these networks will yield better orthology predictions than sequence similarity alone. Recent work has found that existing aligners have difficulty making use of both topological and sequence similarity when aligning, with either one or the other being better matched. This can be at least partially attributed to the fact that existing aligners try to combine these two potentially conflicting objectives into a single objective.