I know like to determine which specific positions in two coevolving proteins are coevolving. One can already determine which positions within a protein are coevolving through methods such as mutual information. If I wanted to extend this to positions within two protein families instead of just one, could I simply the append the sequences in the msa of the first protein family to the sequences in the msa of the second protein family? For example, let's say I have two families, A and B, and only two species in each, 1 and 2. Can I input (A1+B1) and (A2+B2) into an inter-residue algorithm?
I apologize if this question doesn't make sense. I'm very new to bioinformatics and biology research in general.