How to calculate the mutual information (MI) between two sites on a protein sequence?

Question

[Bjoux]

How to calculate the mutual information (MI) between two sites on a protein sequence? what I need is a standalone tool or python script. Thanks.

[Joe]

I don’t really understand what you mean by mutual information? Can you elaborate?

Answer 1

[Jean-Karim Heriche]

Mutual information is a concept from information theory that aims at quantifying how dependent two variables are. On multiple sequence alignments, it can be used to identify co-evolving sites and can be computed from the column entropy. This paper may be relevant. MI for alignments can be computed with the R package BioPhysConnectoR

[Joe]

Ah OK, I wasn't sure if it was an actual term or not but guessed it would probably be related to the column entropy.