Inferring site rates

[PhyloStar]

I could get the site rate for each site using the report siterates=yes command. Does the sampled site rate correspond to the mean rate of the category that has the best likelihood for the site?

[nylander]

Dear @PhyloStar , the site rate in the .p file would correspond to the rate accepted by the chain at the point of writing to file, as a weighted average over all rate categories (and not "the mean rate of the category that has the best likelihood for the site"). Not sure if that answered the question...? Yours Johan