{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T20:02:44Z","timestamp":1773259364511,"version":"3.50.1"},"reference-count":37,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2020,2,23]],"date-time":"2020-02-23T00:00:00Z","timestamp":1582416000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["11871061,61828203"],"award-info":[{"award-number":["11871061,61828203"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Entropy"],"abstract":"<jats:p>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\u2013Foulds 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.<\/jats:p>","DOI":"10.3390\/e22020255","type":"journal-article","created":{"date-parts":[[2020,2,24]],"date-time":"2020-02-24T03:33:43Z","timestamp":1582515223000},"page":"255","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Phylogenetic Analysis of HIV-1 Genomes Based on the Position-Weighted K-mers Method"],"prefix":"10.3390","volume":"22","author":[{"given":"Yuanlin","family":"Ma","sequence":"first","affiliation":[{"name":"Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China"},{"name":"School of Economics, Zhengzhou University of Aeronautics, Zhengzhou 450046, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5913-9646","authenticated-orcid":false,"given":"Zuguo","family":"Yu","sequence":"additional","affiliation":[{"name":"Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China"},{"name":"School of Electrical Engineering and Computer Science, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Runbin","family":"Tang","sequence":"additional","affiliation":[{"name":"Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xianhua","family":"Xie","sequence":"additional","affiliation":[{"name":"School of Mathematical and Computer Science, Gannan Normal University, Ganzhou 341000, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guosheng","family":"Han","sequence":"additional","affiliation":[{"name":"Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vo V.","family":"Anh","sequence":"additional","affiliation":[{"name":"Hunan Key Laboratory for Computation and Simulation in Science and Engineering and Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Xiangtan University, Xiangtan 411105, China"},{"name":"Faculty of Science, Engineering and Technology, Swinburne University of Technology, P.O. 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