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examples/TipDate/baseml.ctl

 

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      seqfile = TipDate.phy

 

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     treefile = TipDate.trees

 

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      outfile = mlb

 

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        noisy = 3   * 0,1,2,3: how much rubbish on the screen

 

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      verbose = 0   * 1: detailed output, 0: concise output

 

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        model = 4  * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85, 5:TN93, 6:REV

 

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        clock = 1   * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis

 

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    fix_kappa = 0  * 0: estimate kappa; 1: fix kappa at value below

 

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        kappa = 2.4   * initial or fixed kappa

 

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    fix_alpha = 1  * 0: estimate alpha; 1: fix alpha at value below

 

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        alpha = 0  * initial or fixed alpha, 0:infinity (constant rate)

 

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        ncatG = 8  * # of categories in the dG, AdG, or nparK models of rates

 

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        getSE = 1   * 0: don't want them, 1: want S.E.s of estimates

 

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   Small_Diff = .4e-6

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