codeml, output tree topology different from the input tree

Question

[stolarek.ir]

Dear all,

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.