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CodonTest: Modeling Amino Acid Substitution Preferences in Coding Sequences

Figure 7

Correlations of lower substitution rates and property preservation in the vertebrate rhodopsin alignment.

Model-averaged rates were stratified by whether or not they involved a change in polarity, charge or Stanfel class, the medians of two rate distributions were compared using a one sided Wilcoxon rank-sum test. We further correlated the magnitude of substitution rates with one of five property-based distances between the corresponding residues (defined in [18]) using a one-sided (negative correlation) Pearson product-moment correlation test.

Figure 7