Estimated parameters for Mutation-Selection model

[Tae-Kun Seo]

Dear Ziheng, 

I'm trying to look at estimated parameters with Mutation-selection model of Yang and Nielsen (2008) after running codeml program.   It seems that file "rst" contains relevant information, but I have difficulty in understanding the meaning of column names.  "2Ns_IJ" is easy to understand because it is  well-defined in the paper as "F_J - F_I", but I don't know how the other measures (pMut_IJ, pSub_IJ, FSub(CodonUsage), FSubw(after w), etc) correspond to the definition in the paper.  More specifically, I want to see estimates of each nucleotide frequencies and F_J of eqn(4) of Yang and Nielsen(2008). How can I derive this information from "rst" file? 

I would greatly appreciate your help. 

Sincerely,

Tae-Kun Seo