Phylogenetic Analysis of HIV-1 Genomes Based on the Position-Weighted K-mers Method.

ABSTRACT: HIV-1 viruses, which are predominant in the family of HIV viruses, have strong pathogenicity and infectivity. They can evolve into many different variants in a very short time. In this study, we propose a new and effective alignment-free method for the phylogenetic analysis of HIV-1 viruses using complete genome sequences. Our method combines the position distribution information and the counts of the k-mers together. We also propose a metric to determine the optimal k value. We name our method the Position-Weighted k-mers (PWkmer) method. Validation and comparison with the Robinson-Foulds distance method and the modified bootstrap method on a benchmark dataset show that our method is reliable for the phylogenetic analysis of HIV-1 viruses. PWkmer can res

SUBMITTER: Ma Y 

PROVIDER: S-EPMC7516702 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature