Figure 4

Excerpt from the single linkage tree The superfamily of sequence O93431 is determined as follows (traversing the tree along the branches depicted as bold lines). The first internal node connects this sequence with the four sequences P52794, P20827, P52793, and P97553 at an E-value of 1e-52. Thus, the ratio of the size of the merging subtree and the size of the current subtree at this point is 4/1. Stepping up the hierarchy, the next node (E-value 4e-38) connects these five sequences with a subtree consisting of 13 sequences, resulting in a ratio of 13/5 (= 2.6). Stepping further up the hierarchy, the following ratios are 1/18 (= 0.056 at E-value 6e-38), 2/19 (= 0.105 at E-value 2e-37), 15/21 (= 0.714 at E-value 2e-13), 1/36 (= 0.028 at E-value 5e-10), 211 975/37 (= 5729.054 at E-value 0.022), 259/212 012 (= 0.001 at E-value 0.023), etc. Taking the maximum of the ratios we find the superfamily root at E-value 5e-10 as the last node before the largest relative increase (depicted as a bullet in the tree). The superfamily of sequence O93431 hence consists of the 37 sequences belonging to the ephrin type A and type B families plus a few predicted proteins.