In this paper, we propose a new method for inferring functional relationships between proteins from their phylogenetic profiles. The Evolutionary Bond Energy Algorithm (EBEA) enhances the greedy BEA clustering algorithm with evolutionary search -genetic algorithms. We conducted a series of experiments using phylogenetic profiles provided by the Cluster of Orthologous Groups of Proteins (COG) database. Experimental results demonstrate that the proposed method is able to infer meaningful clusters of functionally related proteins.
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