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

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

Yuan-Lin Ma, Zu-Guo Yu, Runbin Tang, Xianhua Xie, Guosheng Han, Vo V. Anh

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 resolve within-group variations for different known subtypes of Group M of HIV-1 viruses. This method is simple and computationally fast for whole genome phylogenetic analysis.

2020

alignment-free, HIV-1 virus, Phylogenetic analysis, position-weighted <i>k</i>-mers, robinson–foulds distance

DOI: 10.3390/e22020255

Entropy

MDPI AG

Science, Astrophysics, Physics

EN