AIS (Almost Invariant Sets) is a program which uses a novel criterion and method to classify amino acids. The goal is to identify sets of amino acids with a high probability of change between elements of the set but small probability of change between different sets by using amino acid replacement matrices and their eigenvectors. After identification of the subsets the quality of the partition is assessed with a conductance measure
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Kosiol et al. (2004),
A new criterion and method for amino acid classification
Journal of Theoretical Biology 228:97-106.