Classification of amino acids induced by their associated matrices

In this paper we carry out an analysis of different types of potential and substitution matrices for amino acids, oriented to give a classification of the latter. The cluster decomposition is obtained, in a fully unsupervised way, from the subdominant ultrametric associated to the distance between amino acids induced by the corresponding matrix. In the comparative study, by looking at the classifications obtained from diverse matrices, we can get information on how they account for the different chemical-physical properties of the amino acids. (c) 2004 Elsevier B.V. All rights reserved.