A new distance metric and its application in phylogenetic tree construction

Most methods for phylogenetic tree construction are based on multiple sequences alignment, but alignment often fails to work when the datasets become large and complex. Recently, a variety of efforts have been made to derive alignment-free methods to overcome this limitation. In this work, we propose a new distance metric based on the diversity increment between sequences. The distance matrix calculated by this metric can be used to construct phylogenetic trees. When using our method to construct the phytogeny of eutherian orders from the comparison of whole mtDNA sequences, we got rather good results. We also tested our method on the complete genome sequences of SARS coronavirus, the result tree is the same as what had been obtained by DNASIS, whereas the experiment illustrates that our method is much more efficient and automatic.