Hi all,

I am using codeml in PAML (Phylogenetic Analysis by Maximum Likelihood) to test sites under positive selection in a particular lineage. A summary of my parameters in ctl files is pasted below. I did the codon based alignment using PRANK, ran the codeml, did a log rank test with degree of freedom 1.

I noticed that in some (rare) cases the log rank test is significant but a few sites with significant bayes emperical bayes probability of selection are conserved i.e. the amino acid in alignment is same in all species. I am confused by the output! How can a site be under positive selection if there is no change in the amino acid in alignment ? Are these false positives or is there an alternative interpretation?

My guess is that these are false positives but I may be missing something. Any help is greatly appreciated!

- Urjaswita

My parameters in ctl files:

----------- positive --------

seqtype = 1      * 1:codons
CodonFreq = 2      * 0:equal, 1:F1X4, 2:F3X4, 3:F61
model = 2      * 2:user specified dN/dS ratios for branches 1:separate omega for each branches 0:one omega ratio for all branches 
NSsites = 2      * M2a(null)
icode = 0      * 0:universal code
fix_kappa = 0      * 1:kappa fixed, 0:kappa to be estimated
kappa = 2      * initial or fixed kappa
fix_omega = 0      * 1:omega fixed, 0:omega to be estimated 
omega = 1      * initial omega

---------- null -------------

seqtype = 1      * 1:codons
CodonFreq = 2      * 0:equal, 1:F1X4, 2:F3X4, 3:F61
model = 2      * 2:user specified dN/dS ratios for branches 1:separate omega for each branches 0:one omega ratio for all branches 
NSsites = 2      * M2a(null)
icode = 0      * 0:universal code
fix_kappa = 0      * 1:kappa fixed, 0:kappa to be estimated
kappa = 2      * initial or fixed kappa
fix_omega = 1      * 1:omega fixed, 0:omega to be estimated 
omega = 1      * initial omega