ASaturA discriminates amino acid substitutions with high and low probabilities of occurrence.ASaturA sorts all substitutions according to these probabilities and a probability ‘cut-off’ value can be chosen that differentiates between frequent and rare substitutions. For each sequence pair, the program plots the number of observed frequent and rare aa replacements against their evolutionary distance. By modifying the substitution probability ‘cut-off’ value, the number of aa substitutions classified as frequent or rare can be changed. Ideally, careful selection of the ‘cut-off’ value splits the original data set into a saturated and an unsaturated one. Besides the most widely used substitution probability matrices, such as PAM, BLOSUM, mtREV24 and JTT, user-defined matrices can be used also.
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Van de Peer, Y., Frickey, T., Taylor, J.S., Meyer, A. (2002)
Dealing with saturation at the amino acid level: A case study involving anciently duplicated zebrafish genes.
Gene 295, 205-11.