Fig. 4.

Gap configurations of local MSAs examined in perturbation analyses. a The 3-OTU tree used in the perturbation analyses. A node (open circle) is labeled n _i (i = 1,2 or 3) (external) or n ^Root (root). A branch is labeled b _i (i = 1,2 or 3). In the following, ∆L ^Di denotes the number of sites that the sequence at node n _i has between the PASs. b Local gap configuration in case (I). c Case (II) with ΔL ^D1 = ΔL ^D2 = 5. d Case (III) with ΔL ^D1 = 5. e Case (IV) with ΔL ^D1 = 5 and ΔL ^D2 = 3. The figure is a modified version of Figure 4 of [43]