A mutation matrix, denoted by M , describes the probabilities of amino acid mutations for a given period of evolution. 1- M ii then represents the probability of mutating away from i . This is a Markovian model and, while simple, it is one of the best methods available for modeling evolution. Intrinisic properities of amino acids, like hydrophobicity, size, charge, etc. can be modelled by appropriate mutation matrices. However, we can not model dependencies which relate one amino acid characteristic to the characteristics of its neighbours.
Amino acids appear in nature with different frequencies.
We can not distinguish between a mutation from i into j and a mutation from j into i .