Figure 5.

Ability of the different methods to recover published convergent sites in two empirical alignments. Those alignments had been used to study convergent transitions from C3 to C4 metabolisms in plants ((a) Besnard et al. [20] found 16 convergent sites in Cyperaceae, (b) Parto & Lartillot [24] found 15 convergent sites in Amaranthaceae). For each method, the scores were obtained for each site of the alignment. The sites were then ranked according to their scores, and only the ranks of previously published convergent sites are reported on the figure.