eeob563/M3codeml.ctl at master · jaquethjs/eeob563 · GitHub

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      seqfile = 98_aln.paml
     treefile = 98_NAM_aa_nj.tree
      outfile = 98-NAM_3_results


outfile = results.txt           * main result file name
        noisy = 9                     * lots of rubbish on the screen
      verbose = 1                     * detailed output
      runmode = 0                     * user defined tree
      seqtype = 1                     * codons
    CodonFreq = 2                     * F3X4 for codon ferquencies
        model = 0                     * one omega ratio for all branches

    * NSsites = 0                     * SET THIS for M0
    * NSsites = 1                     * SET THIS for M1
    * NSsites = 2                     * SET THIS for M2
      NSsites = 3                     * SET THIS for M3
    * NSsites = 7                     * SET THIS for M7
    * NSsites = 8                     * SET THIS for M8

        icode = 0                     * universal code
    fix_kappa = 1                     * kappa fixed
      * kappa = 4.43491               * SET THIS to fix kappa at MLE under M0
      * kappa = 4.39117               * SET THIS to fix kappa at MLE under M1
      * kappa = 5.08964               * SET THIS to fix kappa at MLE under M2
        kappa = 4.89033               * SET THIS to fix kappa at MLE under M3
      * kappa = 4.22750               * SET THIS to fix kappa at MLE under M7
      * kappa = 4.87827               * SET THIS to fix kappa at MLE under M8

    fix_omega = 0                     * omega to be estimated
        omega = 5                     * initial omega

        ncatG = 3                     * SET THIS for 3 site categories under M3
      * ncatG = 10                    * SET THIS for 10 of site categories under M7 and M8

  fix_blength = 2                     * fixed branch lengths from tree file