Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference.

As expected, we observe an excess of sites with high values of -ln(PIP n ) in real data, whereas the number of sites that show a medium value of -ln(PIP n ) is higher for the simulated data; results are highly significant (Kolmogorov-Smirnov test, p < 2.2e -16 for both datasets).

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