4 treefile = HIV2ge.tre
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7 seqtype = 0 * 0: nucleotides; 1:codons; 2:AAs
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8 usedata = 0 in.BV.HKYG5 * 0: no data; 1:seq like; 2:use in.BV; 3: out.BV
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10 ndata = 1 * 3 for mt2G3P and 6 for 4G6P
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11 clock = 1 * 1: global clock; 2: independent rates; 3: correlated rates
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12 TipDate = 1 100 * TipDate (1) & time unit
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14 RootAge = B(0.5, 2.0, 0.01, 0.01) * used if no fossil for root
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15 * RootAge = B(2.9, 3.1, 0.01, 0.01) * used if no fossil for root
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16 * RootAge = B(0.2, 1.5, 0.01, 0.01) * used if no fossil for root
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17 * RootAge = B(0.8, 2.5, 0.01, 0.01) * used if no fossil for root
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19 model = 4 * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
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20 aaRatefile = wag.dat
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21 alpha = 0.5 * alpha for gamma rates at sites
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22 ncatG = 5 * No. categories in discrete gamma
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24 cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
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26 BDparas = 2 1 0 1.8 * lambda, mu, rho, psi for birth-death-sampling model
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27 kappa_gamma = 6 2 * gamma prior for kappa
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28 alpha_gamma = 1 1 * gamma prior for alpha
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30 rgene_gamma = 2 10 2 * gammaDir prior for rate for genes
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31 sigma2_gamma = 2 2 1 * gammaDir prior for sigma^2 (for clock=2 or 3)
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32 finetune = 1: 0.5 0.2 .1 .05 .05 .05 * auto (0 or 1): times, musigma2, rates, mixing, paras, FossilErr
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