dN/dS analysis of genomes
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2.9 years ago
Mehmet ▴ 670

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?

genome sequence alignment • 1.7k views
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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.

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

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Maybe by setting mgene = in the control file?

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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

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When I typed grep omega mlc > omega.txt

omega.txt file has nothing.

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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".

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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?

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I think that should work.

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