Protocols and Methods for the in Silico Reconstruction of the Origin and Evolution of Metabolic Pathways

It is possible to reconstruct the origin and evolution of metabolic pathways by inferring useful hints from the analyses of metabolic pathways existing in contemporary cells. Several bioinformatic tools allow the comparison of gene and genomes from organisms belonging to the three cell domains, giving rise to comparative genomics. Moreover the storage, the interpretation and the integration of several sources of information (gene structure and organization, gene regulation, protein-protein interactions) make possible to infer phylogenetic relationships among organisms, leading to a new approach referred to as phylogenomics. A short description of several tools is reported.