what is wrong with my codeml control file? and how can i estimate kappa?

[Guillermo Gerardo Hernandez Robles]

Hi.

my name is Guillermo.

I have a problem with my codeml control file. i used a concatenated sequence of 10 mitochondrial coding genes, with the format option G, and a species tree that was build it with *BEAST.

I want to do a selection analysis to detect neutral and positive selection in the nucleotide sequence, so i went with site-model. According to the manual i can run several analysis but i get this error: Error: "NSsites with ngene.."

This is my control file:

      seqfile = NucSeqMit.nuc    * sequence data file name
     treefile = SpTreeMit16sp.tree   * tree structure file name

      outfile = mlc          * main result file name
        noisy = 3   * 0,1,2,3,9: how much rubbish on the screen
      verbose = 0   * 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
        clock = 1   * 0: no clock, unrooted tree, 1: clock, rooted tree
       aaDist = 0   * 0:equal, +:geometric; -:linear, {1-5:G1974,Miyata,c,p,v}
        model = 0

      NSsites = 0 1 2 * 0:one w; 1:NearlyNeutral; 2:PositiveSelection; 3:discrete;
     
                    * 4:freqs; 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ10:3normal
        icode = 0   * 0:standard genetic code; 1:mammalian mt; 2-10:see below
        Mgene = 1   * 0:rates, 1:separate; 2:pi, 3:kappa, 4:all

    fix_kappa = 0   * 1: kappa fixed, 0: kappa to be estimated
        kappa = 1   * initial or fixed kappa
    fix_omega = 0   * 1: omega or omega_1 fixed, 0: estimate
        omega = 1.3  * initial or fixed omega, for codons or codon-based AAs
        ncatG = 10   * # of categories in the dG or AdG models of rates

        getSE = 0   * 0: don't want them, 1: want S.E.s of estimates
 RateAncestor = 0   * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)

   Small_Diff = .45e-6
    cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?
  fix_blength = 0  * 0: ignore, -1: random, 1: initial, 2: fixed

and my sequence file looks like this screen-capture.

what am i doing wrong?

and how do i know im using the right value of Kappa?

Thanks in advance.

[Ziheng]

you can't use option G together with the NSsites model.  

ziheng