Dear all,

I am new to this. I am using the ASR algorithm to reconstruct ancestral sequences. I wanted to know, out of the three types of sequences generated by the program (marginal, joint and sampled), which is the most reliable one? Does this solely depend on the support values for each type? Can I rely on these sequences to evaluate the selection regimes for the particular clade the sequence represents?

Thank you very much,
Kartik

Dear Sir,

Thank you very much for the reply.

What I meant was, I wanted to construct a homology model for the ancestral sequences and infer the sites/domains under selection so that I could compare it with the extant proteins. Is that inappropriate?

Thank you very much,
Kartik 

Thank you for the help.

Best,
Kartik