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. 2011 Mar 18;6(3):e17244. doi: 10.1371/journal.pone.0017244

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Sanzo Miyazawa.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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Each element log- of the log-odds matrix corresponding to (A) single, (B) double, and (C) triple nucleotide changes in the ML-200 model fitted to the 1-PAM KHG codon substitution matrix is plotted against the log-odds log- calculated from KHG. In (D), codon log-exchangeabilities of the 1-PAM KHG codon substitution matrix corresponding to triple nucleotide changes are plotted against the log-odds log- calculated from KHG. The log-exchangeability of the 1-PAM KHG is defined as . Upper triangle, plus, circle, and cross marks show the log-odds values for synonymous pairs and one-, two-, and three-step amino acid pairs, respectively. Log-exchangeabilities for the codon pairs whose instantaneous rates are estimated to be in KHG are shown to be about in this figure. The dotted line in each figure shows the line of equal values between the ordinate and the abscissa.

Inline graphic — Each element log- of the log-odds matrix corresponding to (A) single, (B) double, and (C) triple nucleotide changes in the ML-200 model fitted to the 1-PAM KHG codon substitution matrix is plotted against the log-odds log- calculated from KHG. In (D), codon log-exchangeabilities of the 1-PAM KHG codon substitution matrix corresponding to triple nucleotide changes are plotted against the log-odds log- calculated from KHG. The log-exchangeability of the 1-PAM KHG is defined as . Upper triangle, plus, circle, and cross marks show the log-odds values for synonymous pairs and one-, two-, and three-step amino acid pairs, respectively. Log-exchangeabilities for the codon pairs whose instantaneous rates are estimated to be in KHG are shown to be about in this figure. The dotted line in each figure shows the line of equal values between the ordinate and the abscissa.