Question: Get pvalue and/or confidence interval of dN/dS from the codeml output
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gravatar for Chvatil
9 months ago by
Chvatil40
Chvatil40 wrote:

Hello, I'm actually using the ete3 toolkit package from python in order to run the codeml program from PAML.

So I had :

-1 codon aligned sequences file 
-1 phylogenetic tree

and I was interesting on the dN/dS per branch in my phylogeny, so I got the following output:

branch          t       N       S   dN/dS      dN      dS  N*dN  S*dS

68..69      0.185   1551.6    641.4   0.7845   0.0570   0.0727   88.5   46.6

69..6       0.650   1551.6    641.4   0.7845   0.2005   0.2556  311.1  163.9

69..70      0.123   1551.6    641.4   0.7845   0.0380   0.0485   59.0   31.1

70..71      0.309   1551.6    641.4   0.7845   0.0952   0.1214  147.8   77.9

71..5       0.705   1551.6    641.4   0.7845   0.2175   0.2773  337.5  177.8

71..4       0.367   1551.6    641.4   0.7845   0.1132   0.1443  175.6   92.6

70..72      0.238   1551.6    641.4   0.7845   0.0734   0.0935  113.8   60.0

72..73      0.351   1551.6    641.4   0.7845   0.1084   0.1382  168.2   88.6

73..8       0.431   1551.6    641.4   0.7845   0.1329   0.1695  206.3  108.7

73..9       0.799   1551.6    641.4   0.7845   0.2466   0.3144  382.7  201.6

72..7       0.455   1551.6    641.4   0.7845   0.1403   0.1788  217.7  114.7

68..3       0.914   1551.6    641.4   0.7845   0.2821   0.3596  437.7  230.6

So it seems that I got the maximum likelihood estimate of the dN/dS per branch. But is there any way to get a pvalue associated and/or at least a confidence interval of the estimation of omega?

Thank you for your help.

dnds python • 202 views
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