Fundamentals of Molecular Evolution (2nd edn)

By A. Eyre-Walker. Heredity, 2000

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ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. (2001, methodology): “This method is based on the assumption of equal rates of evolution along all branches of the phylogenetic tree, an assumption that had been repeatedly refuted in the past.(16) Following tree reconstruction, the aligned sequences at each node are compared to construct consensus sequences, a procedure”
Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach (2007, background): “Evolutionary conserved sites may be indicative of active sites or of protein–protein interaction domains, while highly variable sites may represent sites subjected to positive Darwinian selection (1,2).”