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A method based on the 3D graphical representation of gene sequences [B. Liao, J. Mol. Struct.: Theochem.717 (2005) 199-203.] is proposed to analyze the phylogenetic relationships of different genomes. From the 3D curve, we can get a new invariant to characterize the sequences data, then, the evolutionary distances are obtained. An effective method based on the minimum spanning tree is used to construct phylogenetic tree. The evolution and phylogenetic relationship of eight HA (H5N1) genomes of different avian influenza virus illustrate the utility of our approach.