Additional file 3 of Non-Markovian effects on protein sequence evolution due to site dependent substitution rates

Suppl_Figures.pdf. Contains three supplementary figures. Figure S1 (for Appendix), with the test of the Chapman-Kolmogorov equation. Figure S2, with the comparison of the sequence identity as functions of time and of the transition probabilities at the same sequence identity between the Markovian and the non-Markovian dynamics, both for codons and for amino acids. Figure S3 is a panel containing the entry-by-entry comparison of P c (t) and P ~ c ( t ~ ) $\widetilde {P}^{c}(\tilde {t})$ calculated at the same sequence identity for different choice of the shape parameter Îą in the Îł distribution. (PDF 143 kb)