Evaluation of breakpoints predicted by jpHMM and Simplot. We measured the distance between the predicted breakpoints and the real breakpoints as described in the literature. For these distances, we calculated the median value and the interquartile range. A) Inter-subtype artificial recombinants: jpHMM's median is 10, with the interquartile range of 4–15; Simplot's median is 54, with the interquartile range of 19–72 and p < 10-9 in the Wilcoxon signed-rank test. B) Inter sub-subtype artificial recombinants: jpHMM's median values 9, interquartile ranges 3.5–19; Simplot's median values 84, interquartile ranges 19.5–122 and p < 10-7 in the Wilcoxon signed-rank test. In both plots (A and B), the Y -axis represents the number of bases that predicted breakpoints were away from the actual ones. The median values are shown here as the white bars, and the interquartile ranges are shown as the black bars. Numbers in color represent the actual breakpoint positions (every 1000-th nucleotide) in all synthetic recombinants. The duplicated data positions were spread apart in order to show every individual breakpoint here.