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
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