Hi,

I am having some problems to interpret REL results.

I am getting very large coefficients of variation for both dS and dN when applying Nonsynonymous and Dual models to two fragment alignments.
For alignment 1 with Dual I get CV(dS)=4.99 and CV(dN)=5.82 and for alignment 2, something maybe more reasonable,  CV(ds)= 2.09 and CV(dN)=2.84.
Do you have an idea what could be behind this values?

Another problem is: I have applied Yang's REL models to alignment 1 and neutral models are always preferred to selection models (namely in the comparisons M2 vs M1a,M8 vs M7).
M3 is much better than M0 (p<0.0001) and reveals a few positively selected sites. When I apply Dual to the same alignment, first I get the big CVs I mentioned above and consequently
a sign that there is a high synonymous rate heterogeneity (p=0.000) and second the dual model detects a few positively selected sites as well.  Could I assume that M8 and M2 fail to detect selection due to having ignored heterogeneity in dS and take the results of Dual as a sign that selection is occurring? Or should Dual be interpreted  more like a test of the heterogeneity of dS in the sequences than like a selection test?

Thank you very much.

Hi Sergei,

Thank you for your answer.I run my data on datamonkey and here are the results (sorry I couldn't post a url link so I send you a file with the outcome)


Running the data through PARRIS effectively rendered similar results to Paml, namely no positive selection.

I do not really know how to interpret the differences between these groups of tests and how to choose between them. Could you give me your opinion? Thanks a lot.