Get dS numbers _per branch_ with PAML codeml (or branch length estimates)

Question

[BlastedBadger]

Hi, I am trying to estimate divergence times (of genes) in a gene tree, using dS (synonymous substitution rates). At least I am trying to map substitution numbers to branches, then if it corresponds to time is another question.

I am using complete gene trees from Ensembl (one gene tree at a time), including paralog genes, and the corresponding multiple alignements.

I have run codeml using a _free-ratio branch model_ (model=1, NSSites=0). I have trouble understanding if the output is relevant for what I need:

• codeml doesn't actually outputs dS _for each_ branch, but rather a distance matrix, right? (in the file 2NG.dS)
• Plus, the distance matrix in the .mlc and 2NG.dS files is the result from the Nei-Gojobori (1986) method, but (citing the manual) not MLEs [maximum-likelihood estimates] themselves. So are they just rough estimates but codeml can do better?
• Then what exactly is 2NG.t? Time estimates proportional to dS? [EDIT: found it in the "yn00" section of the manual: "number of nucleotide substitutions per codon", i.e. dS and dN combined]
• Do I need to run mcmctree or multidivtimes to estimate branch lengths?

---

PS: I paste here my control file if you need to have a look:

     seqfile = ENSGT00790000122969_genes.phy       * sequence data file name
    treefile = ENSGT00790000122969_genes.nwk       * tree structure file name
     outfile = ENSGT00790000122969.mlc             * main result file name

       noisy = 1   * 0,1,2,3,9: how much rubbish on the screen
     verbose = 1   * 1: detailed output, 0: concise output
     runmode = 0   * 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 = 1   * specifies the number of separate data sets in the file
       clock = 0   * 0: no clock, unrooted tree, 1: clock, rooted tree

      aaDist = 0   * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
                   * 7:AAClasses

       model = 1   * models for codons:
                        * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
                   * models for AAs or codon-translated AAs:
                        * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
                        * 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189)

     NSsites = 0   * 0:one w; 1:neutral; 2:positive 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; 2-11:see below
       Mgene = 0   * 0:rates, 1:separate;

   fix_kappa = 0   * 1: kappa fixed, 0: kappa to be estimated
       kappa = 2.05154 * initial or fixed kappa

   fix_omega = 0   * 1: omega or omega_1 fixed, 0: estimate
       omega = 1

       getSE = 0   * 0: don't want them, 1: want S.E.s of estimates
RateAncestor = 1   * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
  Small_Diff = .5e-6 * small value used in the difference approximation of derivatives

   cleandata = 0   * remove sites with ambiguity data (1:yes, 0:no)?
 fix_blength = 1   * 0: ignore, -1: random, 1: initial, 2: fixed
      method = 0   * 0: simultaneous; 1: one branch at a time

[BlastedBadger]

oops, after reading more on the subject on Biostars, I realized that my codeml run was never properly finishing! It gives an error like Species ENSGT00790000122969.a? that I need to fix first. Will come back when it's done...

Answer 1

[al-ash]

Concerning your 1st question (dS for each branch) - you can find it among the large amount of output information in the outfile (ENSGT00790000122969.mlc in your case) in a tabular form (in section labeled "dN & dS for each branch") and also as branch lengths of your tree in section "dS tree:".