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
