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


#1

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


#2

#3

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).