Dear Sundy,

There is not a direct analogue of PAML's branch-site models on Datamonkey. The closest you can get is to use FEL on a subset of branches within HyPhy. This is discussed in section 2.5.2 of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

As an aside, the reason we don't implement branch-site models is that their statistical behavior may be rather poor (i.e. false positives can be quite high); see section 1.5.2 of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login for an example.

Hope this helps,
Sergei

Dear Sergei,

Could I achieve my purpose by using IFEL model in Datamonkey web server? If I can, how can I define the specific branches I want to investigate? I learned that "IFEL can test sitewise selection on internal branches of the tree."
If what I understand is right, Datamonkey is essentially the same as HYPHY. But I think the web server is much more easier for me to use. I really don't know how to use HYPHY. I know the hyphyBook2007 is very good, but I just have few evolutionary knowledge. I still feel it is difficult to learn how to use HYPHY just by reading. If there are some kind of video, or someone can teach me aside, it may be better
Thank you very much! 

Sundy