Fig. 2.

Phylogenetic profile obtained by using phylpro. The darkened line shows the profile for sequence 12c22 only. Negative peaks for groups A and B (members of which have almost identical profiles) are indicated. The vertical dashed lines extend from the break-point positions identified by lard for 12c22 and the two other group A elements (HKY model, with κ and α estimated from neighbor joining trees for each triplet). P values are calculated from seq-gen using 100 replicates from a Bayesian tree (HKY model: κ, α and base frequencies taken from the tree). The window size in phylpro extends to include 100 variable positions either side of the sliding point. The ordinate shows the linear correlation score of uncorrected pairwise distances from the two windows.