Fig. 6

Two-stage nonparametric and parametric bootstraps. a Examples of two-stage nonparametric and parametric bootstraps from simulated data with high coverage (10X) and filtering (k = 13). The node values give the number of bootstrap trees supporting each node, with the values in parentheses giving bootstraps accounting for only sampling variability (first stage); for each node, the top numbers give the results from the nonparametric bootstrap and the bottom numbers give the results of the parametric bootstrap. Nodes without values all have 100 % support. b like (a) but with low coverage (2X) and without filtering. The ancestral genomes (different between panels) were 80 kbp sequences taken from random starting positions on a 1.9 Mbp sequence of the rabbit genome from Prasad et al. (2008)