Abstract

Background: Existing alignment-based phylogenetic methods remain computationally arduous and even impossible for large numbers of viral genetic sequences.

Objective: Alignment-free methodologies which successfully overcome serious limitations of alignment-based ways, especially for computation time and storage space, have been quickly proposed.

Methods: Natural vector method is a new alignment-free approach for studying phylogenetics. Because of its simplicity when compared with the alignment-based ways, the method has been successfully applied in virus phylogenetic classification lately.

Results: Natural vector method allows us to identify phylogenetic relationships for single-segmented and multiple-segmented viruses at different classification levels such as family, subfamily, genus, species and Baltimore class. The method has high speed and accuracy.

Conclusion: Here we reviewed the development of the natural vector method and discussed its applications on virus phylogenetic classification.

Keywords: Alignment-free, whole genome comparison, nearest neighbour algorithm, Hausdorff distance, natural vector.

Graphical Abstract