mcmctree

最新推荐文章于 2024-08-05 13:27:53 发布

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最新推荐文章于 2024-08-05 13:27:53 发布

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分类专栏：一只想成为战斗鸡的菜鸡文章标签：机器学习人工智能

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baseml.ctl

输入文件：只有根节点标记 @ 时间

   10   1
((((Ccry,Tpse),(Ptri,((Fcyl,Pmul),(nitz4,Nlae)))),(Ngad,Esil)),Igal)'@ 1.9';


      seqfile = ../single-copy.cds.ok.phy.trim * change!!! sequence data file name
      outfile = mlb        * change!!! main result file
     treefile = intree  * change!!! tree structure file name

        noisy = 3   * 0,1,2,3: how much rubbish on the screen
      verbose = 1   * 1: detailed output, 0: concise output
      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
        Mgene = 0   * 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff

    fix_kappa = 0
        kappa = 2   * initial or given kappa

    fix_alpha = 0 
        alpha = 0.5  * initial or given alpha, 0:infinity (constant rate)
       Malpha = 0   * 1: different alpha's for genes, 0: one alpha
        ncatG = 5   * # of categories in the dG, AdG, or nparK models of rates

      fix_rho = 1  
          rho = 0.  * initial or given rho,   0:no correlation
        nparK = 0   * rate-class models. 1:rK, 2:rK&fK, 3:rK&MK(1/K), 4:rK&MK 
      TipDate = 1 10000000 * change!!!    time unit (years)
        clock = 1   * 0: no clock, unrooted tree, 1: clock, rooted tree
        nhomo = 1   * 0 & 1: homogeneous, 2: kappa's, 3: N1, 4: N2
        getSE = 1   * 0: don't want them, 1: want S.E.s of estimates
 RateAncestor = 0   * (1/0): rates (alpha>0) or ancestral states (alpha=0)
    cleandata = 0  * remove sites with ambiguity data (1:yes, 0:no)?

grep -A 1 "Substitution " mlb
rgene_ gamma = a/a a/a^2

mcmctree0.ctl for ML analysis the substitution model

主要是usedata 参数

          seed = -100
       seqfile = ../single-copy.cds.ok.phy.trim
      treefile = ../intree
       outfile = out

         ndata = 1
       seqtype = 0  * 0: nucleotides; 1:codons; 2:AAs
       usedata = 3    * change!!!  0: no data; 1:seq like; 2:use in.BV; 3: out.BV
         clock = 2    * 1: global clock; 2: independent rates; 3: correlated rates
       RootAge = <1.9  * safe constraint on root age, used if no fossil for root.

         model = 0    * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
         alpha = 0    * alpha for gamma rates at sites
         ncatG = 5    * No. categories in discrete gamma

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

       BDparas = 1 1 0    * birth, death, sampling
   kappa_gamma = 6 2      * gamma prior for kappa
   alpha_gamma = 1 1      * gamma prior for alpha
   rgene_gamma = 1 1.25   * change!!!  gamma prior for overall rates for genes
  sigma2_gamma = 1 4.5    * gamma prior for sigma^2     (for clock=2 or 3)

      finetune = 1: 0.1  0.1  0.1  0.01 .5  * auto (0 or 1) : times, musigma2, rates, mixing, paras, FossilErr

         print = 1
        burnin = 2000
      sampfreq = 2
       nsample = 20000

*** Note: Make your window wider (100 columns) before running the program.

mv out.BV in.BV

mcmctree_1.ctl 重复两次

          seed = -1
	  seqfile = ../single-copy.cds.ok.phy.trim 
      treefile = ../intree 
       outfile = out

         ndata = 1
       seqtype = 0  * 0: nucleotides; 1:codons; 2:AAs
       usedata = 2    * 0: no data; 1:seq like; 2:use in.BV; 3: out.BV
         clock = 3    * 1: global clock; 2: independent rates（recommend）; 3: correlated rates
       RootAge = <1.9  * safe constraint on root age, used if no fossil for root.

         model = 0    * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
         alpha = 0    * alpha for gamma rates at sites
         ncatG = 5    * No. categories in discrete gamma

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

       BDparas = 10 10 0    * birth, death, sampling
   kappa_gamma = 6 2      * gamma prior for kappa
   alpha_gamma = 1 1      * gamma prior for alpha

   rgene_gamma = 1 1.25   * gamma prior for overall rates for genes
  sigma2_gamma = 1 4.5    * gamma prior for sigma^2     (for clock=2 or 3)

      finetune = 1: 0.1  0.1  0.1  0.01 .5  * auto (0 or 1) : times, musigma2, rates, mixing, paras, FossilErr

         print = 1
        burnin = 8000
      sampfreq = 2
       nsample = 30000

*** Note: Make your window wider (100 columns) before running the program.

查看 out 文件，制作后验时间拟合曲线，check 结果