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Figure 4 | BMC Evolutionary Biology

Figure 4

From: Phylogenetic inference under varying proportions of indel-induced alignment gaps

Figure 4

Pairwise comparison of inference methods under MD gap treatment. values are compared, in a pairwise fashion, for four inference methods: NJ, PhyML, and MP. As elsewhere, the left and right columns refer to the 1:1 and 1:3 insertion-deletion rate ratios. In each panel, the average phylogenetic accuracy, , for one inference method is plotted against that of another. The dots in each graph are color coded to reflect the gap percentage (G/S %) against which the values have been measured, ranging from light blue (for the lowest G/S values) to red (for the highest G/S values); see legend below figure. 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 paired t-test (p < 0.05) results are shown with a letter (within the dot) that signifies if a particular method is statistically better than the other in a given comparison (J – Neighbor-Joining, P – PhyML, and M – Maximum Parsimony) for the parameter combination. The t-test results that were not statistically significant are presented with no symbol (letter) within each dot. The results of the Z test (p < 0.001) over 110 data points for each method-method comparison is shown with a letter followed by an asterisk (J* – Neighbor-Joining, P* – PhyML, and M* – Maximum Parsimony)

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