Phylogenetic relationships of eight malaria parasites. Phylogenetic tree reconstructions were based on 218 proteins. The single alignments were concatenated to form a super-alignment and problematic alignment regions were subsequently removed with Gblocks. This procedure resulted in an alignment with 49,521 aa positions (no missing data), which was used for ML tree reconstruction and Bayesian tree search. T. gondii, C. parvum, T. annulata, and B. bovis were used as an outgroup to root the tree. Only the ML tree is displayed, but the topology of the Bayesian tree was identical. Numbers at the nodes denote bootstrap support values (left) and Bayesian posterior probabilities (right). The scale bar equals 0.05 expected substitutions per site. See also Additional files 1, 2 and 3.