Codeml file and output

Question

[Mehmet]

Dear all,

I have performed genome wide dN/dS analysis of orthologs of six species.

Briefly, 1. orrthofinder for orthologs 2.pal2aln for codon-based alignment. 3.Codeml for dN/dS analysis.

in codeml file: I selected runmode=2, therefore I did not provide a user tree file.

After getting results, I saw there is no omega (dN/dS) value in the output file.

the output file has many best tree results, of all orthologs.

My question is how can I get omega value from the result file? and is it fine to select tree file from the output and use it in next codeml run as a "user tree file" ?

for selection the tree file; is it fine to use best tree that has highest log value?

Here is codeml file:

seqfile = all.paml      * sequence data filename
  outfile = mlc           * main result file name

  runmode = 2  * 0: user tree;  1: semi-automatic;  2: automatic
               * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise

  seqtype = 1  * 1:codons; 2:AAs; 3:codons-->AAs
CodonFreq = 2  * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table

    ndata = 5398 * number of gene alignments to be analysed
    clock = 0  * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis

    model = 0  * models for codons: 0:one, 1:b, 2:2 or more dN/dS ratios for branches

  NSsites = 0  * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
               * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
               * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
               * 13:3normal>0

    icode = 0  * 0:universal code; 1:mammalian mt; 2-10:see below

fix_omega = 0  * 1: omega or omega_1 fixed, 0: estimate 
    omega = .4 * initial or fixed omega, for codons or codon-based AAs

cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?

• Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,
• 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt.,
• 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt.,
• 10: blepharisma nu.
• These codes correspond to transl_table 1 to 11 of GENEBANK.

Thank you.