Comparison between site likelihoods when Aquificales are placed close to Epsilon-proteobacteria and when they are placed with Thermotogales. Upper panel: summed differences between site log-likelihoods obtained when Aquificales are placed with epsilon-Proteobacteria and when they are placed with Thermotogales. A descending trend means that a consecutive series of sites favours the Thermotogales position (T signal), whereas an ascending trend means that a series of sites favours the epsilon-proteobacterial position (E signal). Genes have been ordered according to their position along the Aquifex genome. Dashed blue lines represent gene boundaries. The red interval represents the genes which appear to contain most of the E signal. The green interval represents gene infB, in which the curve first decreases and then increases. Lower panel: result obtained by the Maximum Predictive Partitioning algorithm when asked to find the most likely partition of the sites in two segments. The a posteriori most likely model for the first segment is the tree in which Aquificales are sister group to Thermotogales, and the second segment is best fitted by the tree in which Aquificales are sister group to epsilon-Proteobacteria.