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!

Hi Matt,


Quote:

is the program saying with the part about selective regimes?

This means that EITHER proportions or omega values (or BOTH) for positively selected classes differ between the two data sets. The next two tests, as you correctly surmised, test each component separately.


Quote:

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

Yes; the entire distribution is considered for this test (negative, neutral and positive classes)

Cheers,
Sergei

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)

Dear Matt,

There really is no explicit consideration of effective population sizes in this comparative phylogeny based approach. One can construct arguments about the relative rate of mutations and fixations (see some of the papers by Ziheng Yang and Rasmus Nielsen on that account), in inter-species comparisons, but that's about it.

Sergei