I hope this question makes sense. I have a multiple sequence alignment and I'd like to propose positions that could have a functional relevance. Some positions are fully, or almost fully, conserved and I can quantify the conservation by means of Shannon entropies.
However, I've found out that some people is measuring evolutionary rates of positions, for example with Rate4Site. Here, slowly evolving positions are thought to be relevant. To what extend this notion is different from residue conservation? If I want to find residues that may have functional or structural relevance, what would you guys measure?