Figure 1

Simulation setup A and B. Two sets of nucleotide and amino acid data using a) 4-taxon (setup A) and b) 6-taxon topologies (setup B). Setup A contained two elongated, non directly related terminal branches (B L 2 = 0.1,0.3,0.5,0.7,0.9,1.1,1.3,1.5) under three different branch length conditions of remaining short branches (B L 3 = 0.1,0.12,0.14 and R B = 0.1) and two different lengths of the very short internal branch (B L 1 = 0.01,0.02). Setup B contained two elongated internal branches (B L 2 = 0.1,0.3,0.5,0.7,0.9,1.1,1.3,1.5), separated by a short internal branch (B L 1 = 0.01) while terminal branches are kept constant (B L 3 = 0.01 and R B = 0.1).