Before revision:  In this paper, we present the first alignments of large networks based solely upon detailed network topology, and demonstrate that both species phylogeny (the ``tree of life'') and detailed biological function of individual proteins can be extracted from topological comparisons of biological networks. Our phylogenetic trees provide a new and independent source of phylogenetic information.
After revision:  In this paper, we present the first alignments of large networks based solely upon detailed network topology, and demonstrate that both species phylogeny (the ``tree of life'') and detailed biological function of individual proteins can be extracted from a solely topological comparison of networks. Topological alignments provide an independent new source of phylogenetic information.