PAML: Codeml Foreground/background branch issue

Question

[j.a.yearsley]

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!

[rs]

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?