Question: PAML: Codeml Foreground/background branch issue
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gravatar for j.a.yearsley
2.4 years ago by
j.a.yearsley10
European Union
j.a.yearsley10 wrote:

Hi All,

I have tried to find the answer already here but I cannot. If it has already been asked then I apologise and please show me to the right one!

I'm currently using the PAML branch-site model (Model = 2, NSsite= 2) to detect whether certain proteins of interest are showing signs of positive selection.

The analysis requires that I specify background branches and foreground branches. There is no biological reason why there should be any difference in selection between any of my branches. How do I just carry my analysis out for everything?

Thanks in advance!

paml • 868 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by j.a.yearsley10

This is maybe a silly question on my part but if you're not expecting there to be differences in selection between branches, then why would you want to use a branch model?

ADD REPLYlink written 21 months ago by rs40
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