1 seqfile = stewart.aa * sequence data filename
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2 treefile = stewart.trees * tree structure file name
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3 outfile = mlc * main result file name
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5 noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
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6 verbose = 1 * 0: concise; 1: detailed, 2: too much
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7 runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic
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8 * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise
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10 seqtype = 2 * 1:codons; 2:AAs; 3:codons-->AAs
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11 CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
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14 clock = 0 * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
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15 aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
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16 aaRatefile = dat/jones.dat * only used for aa seqs with model=empirical(_F)
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17 * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
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20 * models for codons:
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21 * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
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22 * models for AAs or codon-translated AAs:
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23 * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
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24 * 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)
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26 NSsites = 0 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs;
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27 * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
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28 * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1;
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31 icode = 0 * 0:universal code; 1:mammalian mt; 2-10:see below
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33 * codon: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
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34 * AA: 0:rates, 1:separate
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36 fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
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37 kappa = 2 * initial or fixed kappa
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38 fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
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39 omega = .4 * initial or fixed omega, for codons or codon-based AAs
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41 fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
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42 alpha = 0. * initial or fixed alpha, 0:infinity (constant rate)
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43 Malpha = 0 * different alphas for genes
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44 ncatG = 8 * # of categories in dG of NSsites models
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46 getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
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47 RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
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50 cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)?
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51 * fix_blength = -1 * 0: ignore, -1: random, 1: initial, 2: fixed
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52 method = 0 * Optimization method 0: simultaneous; 1: one branch a time
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54 * Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,
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55 * 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt.,
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56 * 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt.,
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57 * 10: blepharisma nu.
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58 * These codes correspond to transl_table 1 to 11 of GENEBANK.
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