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seqfile = lysozymeSmall.txt
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treefile = lysozymeSmall.trees
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noisy = 9 * 0,1,2,3,9: how much rubbish on the screen
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verbose = 1 * 1: detailed output, 0: concise output
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runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic
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* 3: StepwiseAddition; (4,5):PerturbationNNI
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seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs
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CodonFreq = 2 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table
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clock = 0 * 0: no clock, unrooted tree, 1: clock, rooted tree
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* 0:one, 1:b, 2:2 or more dN/dS ratios for branches
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NSsites = 0 * dN/dS among sites. 0:no variation, 1:neutral, 2:positive
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icode = 0 * 0:standard genetic code; 1:mammalian mt; 2-10:see below
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fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated
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kappa = 2 * initial or fixed kappa
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fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate
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omega = 2 * initial or fixed omega, for codons or codon-transltd AAs
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fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha
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alpha = .0 * initial or fixed alpha, 0:infinity (constant rate)
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Malpha = 0 * different alphas for genes
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ncatG = 4 * # of categories in the dG or AdG models of rates
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getSE = 0 * 0: don't want them, 1: want S.E.s of estimates
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RateAncestor = 0 * (1/0): rates (alpha>0) or ancestral states (alpha=0)
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method = 0 * 0: simultaneous; 1: one branch at a time
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* Specifications for duplicating results for the small data set in table 1
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* of Yang (1998 MBE 15:568-573).
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* see the tree file lysozyme.trees for specification of node (branch) labels
added
removed
examples/lysozyme/lysozymeSmall.ctl
