Fig. 6From: General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computationSimulation analyses on absolute alignment frequencies. Each panel compares the predicted absolute frequency of each local homology structure (ordinate) against the number of times that it actually occurred in a simulated dataset (abscissa). The predicted absolute frequency was calculated using Eq. (SM-7.1) in Additional file 1. Note the logarithmic scaling for both axes, which tends to exaggerate sampling errors on the lower-left region in each panel. Panels a, b and c, respectively, show the results with the simulated sets 1A, 1B and set 1B after removing long gapped segments. The panels a-c are reformatted versions of panels A-C of Figure 29 of [48]Back to article page