Methods
Methods for estimating Ka and Ks use a sequence alignment of two or more nucleotide sequences of homologous protein-coding genes. Methods can be classified into three groups: approximate methods, maximum-likelihood methods, and counting methods. However, unless the sequences to be compared are distantly related (in which case ML methods prevail), the class of method used makes a minimal impact on the results obtained; more important are the assumptions implicit in the chosen method.
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