Question: dN/dS analysis of genomes
0
gravatar for Mehmet
2.5 years ago by
Mehmet630
Japan
Mehmet630 wrote:

Dear All,

I have done several analysis to find dN/dS ratio in six species.

  1. I found one-to-one orthologs (by orthofinder)

  2. I did codon-based alignments of the orthologs that produced .paml format alignments.

  3. I did protein alignment of the orthologs.

Now I would like to have your advice on:

How to concanate all paml files that are used in codeml.?

To be used in codeml (as tree file) do I need to perform phylogenetic of those .paml files? or it is fine to use all.paml files only in codeml?

alignment sequence genome • 1.5k views
ADD COMMENTlink written 2.5 years ago by Mehmet630
1

Hi Mehmet,

I think calculating dn/ds per alignment is good. You can create quick trees for the alignment as input of codeml, otherwise you could let the programme do it.

ADD REPLYlink written 2.5 years ago by Sishuo Wang200

I performed dN/dS analysis using alignments of all orthologs (~5000) together.

ADD REPLYlink written 2.5 years ago by Mehmet630

Maybe by setting mgene = in the control file?

ADD REPLYlink written 2.5 years ago by Sishuo Wang200

Hi Sishuo,

I would like to have your suggestion:

I have run codeml with the control file below;

eqfile = 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.

What I need is how I can get dN/dS ratio

ADD REPLYlink written 2.4 years ago by Mehmet630

When I typed grep omega mlc > omega.txt

omega.txt file has nothing.

ADD REPLYlink written 2.4 years ago by Mehmet630

Hi Mehmet,

Sorry, not sure.

Have you got anything in the mlc file? Or was the analysis disrupted?

By the way, there was a typo in "eqfile = all.paml".

ADD REPLYlink written 2.4 years ago by Sishuo Wang200

the analysis did not disrupt. Yes, I have star tree and best tree values for each gene. But I did not get omega values. Is it fine to use a best tree that has highest likelihood value as a tree file in next codeml run?

ADD REPLYlink written 2.4 years ago by Mehmet630

I think that should work.

ADD REPLYlink written 2.4 years ago by Sishuo Wang200
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