Phylogenetic tree reconstruction from genome-scale metabolic models
  A wide range of applications and research has been done with genome-scale metabolic models. In this work we describe a 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. 
D. Gamermann, A. Montagud, J. A. Conejero, P. F. de C\'ordoba, J. F.   Urchiegu\'ia
q-bio.MN