2 seqfile = examples/DatingSoftBound/mtCDNApri123.txt
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3 treefile = examples/DatingSoftBound/mtCDNApri.trees
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7 seqtype = 0 * 0: nucleotides; 1:codons; 2:AAs
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8 usedata = 1 * 0: no data; 1:seq like; 2:use in.BV; 3: out.BV
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9 clock = 3 * 1: global clock; 2: independent rates; 3: correlated rates
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10 RootAge = <1.0 * safe constraint on root age, used if no fossil for root.
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12 model = 0 * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
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13 alpha = 0 * alpha for gamma rates at sites
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14 ncatG = 5 * No. categories in discrete gamma
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16 cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
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18 BDparas = 1 1 0 * birth, death, sampling
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19 kappa_gamma = 6 2 * gamma prior for kappa
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20 alpha_gamma = 1 1 * gamma prior for alpha
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22 rgene_gamma = 2 2 * gamma prior for overall rates for genes
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23 sigma2_gamma = 1 10 * gamma prior for sigma^2 (for clock=2 or 3)
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25 finetune = 1: 0.1 0.1 0.1 0.01 .5 * auto (0 or 1) : times, musigma2, rates, mixing, paras, FossilErr
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32 *** Note: Make your window wider (100 columns) before running the program.
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