Fig. 2.

Comparison between Markovian and non-Markovian substitution probabilities in the framework of codons and of amino acids. a Points: entry-by-entry comparison of P ^c(t) and ${\tilde{P}}^c\left(t\right)$ in log-log scale, with t=0.235. Each point corresponds to a pair i,j of codons and its x-value is given by $P_{\mathit{\text{ij}}}^c\left(t\right)$, while its y-value is ${\tilde{P}}_{\mathit{\text{ij}}}^c\left(t\right)$. The black squares (zoomed in the yellow inset) are the entries with i=j, while red, green and blue points are respectively the entries where codon i and codon j differ by one, two or three nucleotides. Solid line: line y=x. b Points: entry-by-entry comparison of P ^AA(t) and ${\tilde{P}}^{\mathit{\text{AA}}}\left(t\right)$ in log-log scale, with t=0.23. Coordinates and lines have the same meaning as in panel (a) and colors are such that the entries where i=j are black (zoomed in the yellow inset), while red, green and blue identify the entries with i≠j where the most similar pair of codons coding for amino acids i and j differ respectively by one, two or three nucleotides