seqfile = sim.phy			* sequence data file name

     treefile = ../tree/test_tree.t	* tree structure file name



      outfile = mlc          * main result file name

        noisy = 0   * 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 = 0   * 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

                    * 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 = 0   * 0:rates, 1:separate; 2:pi, 3:kappa, 4:all



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

        kappa = .3   * 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 = 8   * # 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 = 1  * remove sites with ambiguity data (1:yes, 0:no)?

  fix_blength = 0  * 0: ignore, -1: random, 1: initial, 2: fixed