Question: codeml, output tree topology different from the input tree
gravatar for
3.4 years ago by
stolarek.ir650 wrote:

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.

codeml paml • 1.0k views
ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by stolarek.ir650
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1552 users visited in the last hour