1 seqfile = mtCDNApri.nuc
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2 treefile = mtCDNApri.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 = 1 * 0: concise; 1: detailed, 2: too much
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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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12 aaDist = 7 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a
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13 aaRatefile = wag.dat * only used for aa seqs with model=empirical(_F)
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14 * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own
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17 * models for codons:
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18 * 0:one, 1:b, 2:2 or more dN/dS ratios for branches
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19 * models for AAs or codon-translated AAs:
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20 * 0:poisson, 1:proportional, 2:Empirical, 3:Empirical+F
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21 * 6:FromCodon, 7:AAClasses, 8:REVaa_0, 9:REVaa(nr=189)
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23 icode = 1 * 0:universal code; 1:mammalian mt; 2-10:see below
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33 cleandata = 1 * remove sites with ambiguity data (1:yes, 0:no)?
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34 method = 0 * 0: simultaneous; 1: one branch at a time
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