A wide range of applications and research has been done with genome-scale metabolic models. In this work, we describe an innovative methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this comparison in order to infer evolutionary distances between different organisms. Our methodology allows a quantification of the metabolic differences between different species from a broad range of families and even kingdoms. This quantification is then applied in order to reconstruct phylogenetic trees for sets of various organisms.
Keywords: connectivity; genome-scale metabolic models; networks; phylogeny.