How do I compare evolutionary estimates between two sequence groups in codeML?

Question

[codoncity]

I understand that my end result will be a LRT statistic for me to ponder, and I understand that I need to use a branch model. However, I currently don't know how to partition my sequence groups in my codeML control file. I want to see if a certain group (four sequences) is under significantly greater/lesser selective pressure than the remaining sequences in my multiple alignment (5 other sequences). I am a noob when it comes to PAML and so any help would be greatly appreciated.

Answer 1

[shelkmike]

You need to mark branches of one group with "#0" and branches of the second group with "#1" in the tree file that you provide to codeML. See the manual of PAML.
For example: ((some_species_1 #0,some_species_2 #0) #0,(some_species_3 #1,some_species_4 #1) #2,some_species_5 #2);