Entering edit mode
5.1 years ago
Chvatil
▴
130
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.