Commit f9571b75 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 4.9g+dfsg

parent b308d0b8

MCaa.dat

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@@ -8,7 +8,7 @@ 
(((Human:0.06135, Chimpanzee:0.07636):0.03287, Gorilla:0.08197):0.11219, Orangutan:0.28339, Gibbon:0.42389);



.5 8        * <alpha; see notes below>  <#categories for discrete gamma>

2 mtmam.dat * <model> [aa substitution rate file, need only if model=2 or 3]

2 dat/mtmam.dat * <model> [aa substitution rate file, need only if model=2 or 3]



0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 

0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05

MCbase.dat

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 0     * 0,1:seqs or patterns in paml format (mc.paml); 2:paup format (mc.nex); 3: paup JC69 format

 -1234567   * random number seed (odd number)

 1     * 0,1:seqs or patterns in paml format (mc.paml); 2:paup format (mc.nex); 3: paup JC69 format

 -123  * random number seed (odd number)



5 895 100  * <# seqs>  <# nucleotide sites>  <# replicates>

-1         * <tree length, use -1 if tree below has absolute branch lengths>

aaml.ctl

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      seqfile = D:\A\MySoft\paml4.6\stewart.aa

     treefile = D:\A\MySoft\paml4.6\stewart.trees

      seqfile = stewart.aa

     treefile = stewart.trees



      outfile = mlc

        noisy = 9

baseml.ctl

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@@ -7,14 +7,14 @@ 
      runmode = 0   * 0: user tree;  1: semi-automatic;  2: automatic

                    * 3: StepwiseAddition; (4,5):PerturbationNNI 



        model = 7   * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85

        model = 4   * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85

                    * 5:T92, 6:TN93, 7:REV, 8:UNREST, 9:REVu; 10:UNRESTu



        Mgene = 0   * 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff



*        ndata = 100

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

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

    fix_kappa = 0   * 0: estimate kappa; 1: fix kappa at value below; 2: kappa for branches

        kappa = 5  * initial or fixed kappa



    fix_alpha = 0   * 0: estimate alpha; 1: fix alpha at value below
@@ -30,5 +30,5 @@ 
   Small_Diff = 7e-6

    cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?

*        icode = 0  * (with RateAncestor=1. try "GC" in data,model=4,Mgene=4)

*  fix_blength = -1  * 0: ignore, -1: random, 1: initial, 2: fixed

*  fix_blength = 1  * 0: ignore, -1: random, 1: initial, 2: fixed, 3: proportional

       method = 0  * Optimization method 0: simultaneous; 1: one branch a time

codeml.ctl

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@@ -48,7 +48,7 @@ 


   Small_Diff = .5e-6

    cleandata = 1  * remove sites with ambiguity data (1:yes, 0:no)?

*  fix_blength = -1  * 0: ignore, -1: random, 1: initial, 2: fixed

*  fix_blength = 1  * 0: ignore, -1: random, 1: initial, 2: fixed, 3: proportional

       method = 0  * Optimization method 0: simultaneous; 1: one branch a time



* Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,