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James A. Irving, Robert N. Pike, Arthur M. Lesk, and James C. Whisstock
Phylogeny of the Serpin Superfamily: Implications of Patterns of Amino Acid Conservation for Structure and Function
Genome Research December 2000 Volume 10, Number 12 pp. 1845-1864

Figure 8 (A) Flowchart outlining the novel comparison method, used to identify underlying relationships between serpin sequences not apparent from the majority consensus bootstrap tree. The significance threshold of the method was determined empirically: 25–40 serpin-like sequences were derived by “evolving” an ancestral protein along a tree of randomly generated topology. The derived sequences were subjected to bootstrap analysis, followed by the process outlined in the text. The results were then compared with the original tree, and this simulation was repeated 1000 times. It was found that relationships identified by the comparison method with a percentage score greater than 90% were correct more than 99% of the time. (B) Flowchart outlining the tree division method. This procedure was used to identify minor clades that associated with only a limited subset of all major clades in the tree (see Table 4 in text).

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This Article Abstract Full Text Services Email this article to a friend Alert me to new issues of the journal