seqfile = lwsa_FW_k1o05_1030.phy	 ** sequence data filename
     treefile = bel_38_FW.phy	 ** tree structure file name
      outfile = lwsa_FW_k1o05_1030_OUTPUT	 ** main result file name

        noisy = 9  * 0,1,2,3,9: how much rubbish on the screen
      verbose = 0  * 0: concise; 1: detailed, 2: too much
      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
		   ** 4:F1x4MG, 5:F3x4MG, 6:FMutSel0, 7:FMutSel

*	 estFreq = 0 *0: frequency/fitness parameters calculated from observed frequencies in data
		     *1: frequency/fitness parameters estimated by ML from the data (use with FMutSel models)
*        ndata = 10
        clock = 0  * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
       aaDist = 0  * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
   aaRatefile = dat/jones.dat  * only used for aa seqs with model=empirical(_F)
                   * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own

        model = 0
                   ** models for codons:
                       * 0:one, 1:b free ratio, 2:2 or more dN/dS ratios for branches 3:Clade model C
                   * models for AAs or codon-translated AAs:
                       * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
                       * 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)

      NSsites = 0 1 2 3 **0:one w (M0); 1:neutral (M1a); 2:selection (M2a); 3:discrete (M3) ;4:freqs;
                   * 5:gamma; 6:2gamma; 7:beta (M7); 8:beta&w (M8); 9:betaγ
                   * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
                   * 13:3normal>0
				           * 22:M2a_Rel

        icode = 0  * 0:universal code; 1:mammalian mt; 2-10:see below
        Mgene = 0
                   * codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
                   * AA: 0:rates, 1:separate

    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 **fix omega at one in M8 for M8a
        omega = 0.5	 ** initial or fixed omega, for codons or codon-based AAs

    fix_alpha = 1  * 0: estimate gamma shape parameter; 1: fix it at alpha
        alpha = 0 * initial or fixed alpha, 0:infinity (constant rate)
       Malpha = 0  * different alphas for genes
        ncatG = 3  * # of categories in dG of NSsites models

        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 = .5e-6
    cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?
*  fix_blength = -1  * 0: ignore, -1: random, 1: initial, 2: fixed
       method = 1  * Optimization method 0: simultaneous; 1: one branch a time

* 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.