Phylogenetic Analysis with a New Distance Measure

A new distance measure called quadratic divergence distance is used to analyze characteristics between two genome sequences, based on the frequency matrices extracted from Chaos Game Representation (CGR). We generate phylogenetic trees with this distance through Hierarchical Clustering for several complete mitochondrial sequences. And compared with tree generated by CLUSTALW, our program expresses some particular features, which is of significant value of bioinformatics.