Hi All,
I am trying to interpret the results of the dNdSDistribusionComparison.bf.  I have given the program sequence data from 2 species. Here are the results. (Yes, I have read the appropriate parts of hyphybook2007.pdf

[code]Distribution comparison tests

     Are the distributions different?
           LR =      6.886 DF = 10 p =    0.736

     Are selective regimes (dN/dS and proportions) different?
           LR =     31.905 DF = 2 p =    0.000

     Are selection strengths (dN/dS) different?
           LR =     24.546 DF = 1 p =    0.000

     Are the proportions of codons under selection different?
           LR =      0.806 DF = 1 p =    0.369[/code]

The results relating to selection strength and to the proportion of codons is intuitive- but what exactly is the program saying with the part about selective regimes?

About different distributions- does this refer to the distribution of omega across sites?

thanks!

Thanks for the confirmation on the last point- one more question for you!

With regards to the strength of selection, how is effective population size considered? (or is it assumed to be equal in the 2 groups being tested)