Codeml: which substitutions occured in significative sites?
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6.9 years ago
j-blanchard ▴ 10

 Hello everyone,

I used the branch-site method to detect positive selection in a linea with codeml. Now I would like to be sure that the positive selection I detected is really positive selection and not a consequence of BGC. For that, I need to know which substitutions occured in my significative sites. As I have the position of the sites, I just need to know which sequence is used as the ancestral sequence and from that I will deduce what was the substitution.

How can I find which sequence is used as the ancestral sequence?

Thank you a lot,
 

codeml substitutions BGC Ancestral sequence • 1.2k views
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