branch model analysis codeml

Question

[DR]

Hi! I'm trying to observe positive selection events before gene duplication, so I'm performing a branch model analysis. I was wondering if it's essential to incorporate an outgroup. If it's, do you know how divergent should be this outgroup?

Thanks a lot!

Answer 1

[Brice Sarver]

The analyses do not necessarily require an outgroup. However, having an outgroup and using it to root a tree may be required for the type of analysis you're doing. From the PAML manual:

Whether you should use rooted or unrooted trees depends on the model, for example, on whether a molecular clock is assumed. Without the clock (clock = 0), unrooted trees should be used, such as ((1,2),3,4) or (1,2,(3,4)). With the clock or local-clock models, the trees should be rooted and these two trees are different and both are different from (((1,2),3),4). In PAML, a rooted tree has a bifurcation at the root, while an unrooted tree has a trifurcation or multifurcation at the root.

[DR]

Thanks! I used NJ for the topology reconstruction. Do you know if I need to test the molecular clock, or should I just assume clock=0?