Comparison of the phylogenetic trees for protists obtained by genetic sequence alignments and by GRAAL's metabolic network alignments. Left: the tree obtained from genetic sequence comparison. Right: the tree obtained from GRAAL. The following abbreviations are used for species: CHO, Cryptosporidium hominis; DDI, Dictyostelium discoideum; CPV, Cryptosporidium parvum; PFA, Plasmodium falciparum; EHI, Entamoeba histolytica; TAN, Theileria annulata; TPV, Theileria parva. The species are grouped into the following classes: ‘Alveolates,’ ‘Entamoeba,’ and ‘cellular slime mould’.