Phylogenetic tree building using a novel compression-based non-symmetric dissimilarity measure

Abstract

An approach of building phylogenetic trees is to define a distance function based on amino acid sequences of distinct proteins. The aim of this approach is to determine a weighted tree topology that approximates the entire functional similarity relations between proteins, defined by a distance function. In this case - according to the definition - the similarity relation has a symmetric property. However, the assumption of symmetry is not always appropriate, because non-symmetric similarity relations between proteins might have a biological significance. This notion inspired us to define a novel, compressionbased, non-symmetric dissimilarity measure and to modify the ubiquitous 'Unweighted Pair Group Method with Arithmetic Mean' (UPGMA)-based tree-building algorithm so that the new measure can be applied. © 2006, Penkala Bt.