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[Paper] Site-specific rates of evolution, gamma distribution etc


James McInerney and coauthors describe a method of determining site-specific rates of evolution.


The IQ-tree maximum likelihood phylogenetic tree tool includes an option -wsr (write site rate), that writes a .rate file, which looks like this:

Site Rate Category Categorized_rate

1 0.53955 2 0.45293

2 0.46690 2 0.45293

3 0.52875 2 0.45293

4 0.93489 3 0.98634

5 0.70399 2 0.45293


For each site, it prints the posterior-mean rate (2nd column), the category with highest probability that this site belongs to (3rd column) and the rate for that highest category (4th column).