1 seqfile = lysinYangSwanson2002.nuc
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2 treefile = lysin.trees
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4 outfile = mlc * main result file name
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5 noisy = 3 * 0,1,2,3,9: how much rubbish on the screen
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6 verbose = 0 * 1: detailed output, 0: concise output
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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 = 1 * 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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12 model = 0 * codonml: 0:one, 1:b, 2:2 or more dN/dS ratios for branches
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14 NSsites = 0 * 0:one w;1:neutral;2:positive; 3:discrete;4:freqs;
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15 * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ
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16 * 10:beta&1+gamma; 11:beta&1>normal; 12:0&2normal; 13:3normal
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17 icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below
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18 Mgene = 0 * codonml: 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff
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20 fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
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21 kappa = 1.6 * initial or fixed kappa
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22 fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
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23 omega = .8 * initial or fixed omega, for codons or codon-based AAs
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25 ncatG = 3 * # of categories in dG of NSsites models
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27 getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
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30 cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
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31 method = 0 * 0: simultaneous; 1: one branch at a time
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