While running the codeml program of PAML, I gave a blank file as my tree input, and then a proper phylogenetic tree generated using PhyML. For both these files (one blank, and one proper tree), I am getting the same values of pairwise dN and dS (in the output files, 2NG.dN and 2NG.dS). This seems to imply that the codeml program is not using the tree file at all for its calculations.
I would be glad if somebody can help me in identifying the problem.
Thanks in advance, Kushal.