Figure 4.

Example of an outparalog relationship. Two paralogs from B.subtilis (mmgD and citZ) are inparalogs relative to prpC of E.coli, according to Inparanoid. However, the phylogenetic tree shows an outparalog relationship between mmgD and citZ, because the duplication event took place before speciation to B.subtilis and E.coli. Therefore, citZ is not orthologous to prpC. To construct the phylogenetic tree, we first selected from the COG database the specific COG to which mmgD, citZ and prpC belong (6). All homologs, included in this specific COG, were used as input for MUSCLE to construct a multiple sequence alignment (16). Finally, the phylogenetic tree was constructed, from the multiple sequence alignment, using the PHYML algorithm (17).