Greetings,

I am having doubts regarding the detection of coevolution in my 222 protein dataset using Spidermonkey.

I have strongly conserved positions, which however, change in some taxa, but always together. When one of these 4 positions changes, all of them do.

The problem is that once they change, the do not seem to coevolve anymore, and seem to be free to independently mutate.

Therefore, Spidermonkey gives me posterior probabilities of about 0.6. Any advice on analyzing/interpreting these results?

Thanks in advance for your time.

PD: Maybe this should be in theoretical questions?