Figure 7

Effect of the alignment gap percentage on phylogenetic accuracy, number of characters remaining in the alignment, and total alignment length after gap-introduction. The average accuracy, , (dark red circles for the MD treatment, open diamonds for the MLε method, and open circles for the BC treatment), remaining number of characters in the alignment after the gaps are removed (red inverted triangles), and the total length of the alignment (including gaps; symbolized by green, upright triangles), are each shown as a separate function of the average gap percentage, for NJ (Panels A, B), PhyML (C, D), MLε (E, F), Bayesian (G, H), and MP (I, J) inference methods. The left panels show the results for the insertion-deletion rate ratio of 1:1 and the right panels for the ratio 1:3. Each data point in the graph was obtained as the corresponding value for one of all possible combinations of values of r, the substitution rate and λ, the indel rate (see Additional file 1), sequence length (l = 500), transition-transversion rate ratio (κ = 2), and the gamma among-site rate variation shape parameter (α = 0.5), averaged over 100 replicates, for a total of 110 data points in each graph.