I am struggling with understanding the output of the codeml.
I used typical M0 model with settings like so:
runmode = 0 seqtype = 1 CodonFreq = 2 clock = 0 model = 0 NSsites = 0
The provided tree (runmode = 0) is however severely altered in the output tree in the results files from the codeml. When I run branch model and specify the foreground branch of interest, how am I to react to his alteration of my tree topology? The estimated omega value doesn't seem to correspond to the branch I initially intended to estimate it for.