6 分歧时间算不出来结果

程序运行中无报错,但是输出的figtree里面分化时间是NAN。如下:UTREE 1 = (((Spermwhale: -nan, (Cow: -nan, Sheep: -nan)。我用seq模式和近似自然法都是同样的情况,我的序列是cds序列,我输入的树文件是:(((A,(C,S)'U(0.15)')'B(0.47,0.58)',((((B,LA),BK),DR),(H,W))),Ho)'B(0.728,0.783)';我的控制文件如下,请问是哪里出了问题:

seed = -1

       seqfile = single_copy.cds_msa_trimed.phy

      treefile = input.tree

       outfile = out


         ndata = 1

       seqtype = 0  * 0: nucleotides; 1:codons; 2:AAs

       usedata = 1    * 0: no data; 1:seq like; 2:use in.BV; 3: out.BV

         clock = 3    * 1: global clock; 2: independent rates; 3: correlated rates

       RootAge = <0.9  * safe constraint on root age, used if no fossil for root.


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

         alpha = 0.5    * 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 = 1 112   * gamma prior for overall rates for genes

  sigma2_gamma = 1 10    * 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 = 25000000

      sampfreq = 1000

       nsample = 50000000

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2 个回答

omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

检查你的输入文件格式和视频里面是否一致,仔细看看课

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暴雨

attachments-2023-07-GyjPo85z64a6b97076fac.pngattachments-2023-07-MmREkx6P64a6b978281a7.png这是我的输入文件,十分抱歉我没有发现哪里有问题。

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  • 提出于 2023-07-06 20:08

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