1 seqfile = ECP_EDN_15.nuc * sequence data filename
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2 treefile = tree.txt * 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 = 0 * 0: concise; 1: detailed, 2: too much
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7 runmode = 0 * 0: user tree
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9 seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs
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10 CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
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11 clock = 0 * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
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13 * Model C: model = 3 NSsites = 2
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14 * Model D: model = 3 NSsites = 3
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16 model = 3 * 3 = clade models
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17 NSsites = 3 * choose "2" or "3"
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19 icode = 0 * 0:universal code; 1:mammalian mt; 2-10:see below
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21 fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
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22 kappa = 2 * initial or fixed kappa
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24 fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
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25 omega = 0.1234 * initial or fixed omega, for codons or codon-based AAs
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27 fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
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28 alpha = 0. * initial or fixed alpha, 0:infinity (constant rate)
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30 ncatG = 2 * # of categories in dG of NSsites models
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32 getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
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33 RateAncestor = 0 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2)
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36 cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
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