Figure 3

Gap thresholds for different levels of phylogenetic accuracy. The gap thresholds are shown for NJ (Panels A, B), PhyML (C, D), MLε (E, F), Bayesian (G, H), and MP (I, J) methods, for various levels of phylogenetic accuracy. The background in each graph is color-coded to reflect the gap percentage thresholds; see legend at bottom of figure. Each graph also shows values of plotted against different gap thresholds. In Panels E-F, and G-J, white dotted lines refers to the MLε method of Rivas and Eddy (2008), and the Binary Character state (BC) treatment, respectively. The dark red dotted lines refer to the Missing Data (MD) method in all panels. Each value reflects one of all possible combinations of values of substitution rate, r and indel rate, λ, (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. The left panels show the results for the insertion-deletion rate ratio of 1:1 and the right panels for the ratio 1:3.