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For: Xie XH, Yu ZG, Han GS, Yang WF, Anh V. Whole-proteome based phylogenetic tree construction with inter-amino-acid distances and the conditional geometric distribution profiles. Mol Phylogenet Evol 2015;89:37-45. [PMID: 25882834 DOI: 10.1016/j.ympev.2015.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 03/29/2015] [Accepted: 04/06/2015] [Indexed: 11/18/2022]
Number Cited by Other Article(s)
1
Wang T, Yu ZG, Li J. CGRWDL: alignment-free phylogeny reconstruction method for viruses based on chaos game representation weighted by dynamical language model. Front Microbiol 2024;15:1339156. [PMID: 38572227 PMCID: PMC10987876 DOI: 10.3389/fmicb.2024.1339156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/23/2024] [Indexed: 04/05/2024]  Open
2
Tang R, Yu Z, Li J. KINN: An alignment-free accurate phylogeny reconstruction method based on inner distance distributions of k-mer pairs in biological sequences. Mol Phylogenet Evol 2023;179:107662. [PMID: 36375789 DOI: 10.1016/j.ympev.2022.107662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/10/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
3
Redrado S, Esteban P, Domingo MP, Lopez C, Rezusta A, Ramirez-Labrada A, Arias M, Pardo J, Galvez EM. Integration of In Silico and In Vitro Analysis of Gliotoxin Production Reveals a Narrow Range of Producing Fungal Species. J Fungi (Basel) 2022;8:jof8040361. [PMID: 35448592 PMCID: PMC9030297 DOI: 10.3390/jof8040361] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 02/06/2023]  Open
4
Phylogenetic Analysis of HIV-1 Genomes Based on the Position-Weighted K-mers Method. ENTROPY 2020;22:e22020255. [PMID: 33286029 PMCID: PMC7516702 DOI: 10.3390/e22020255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/07/2020] [Accepted: 02/20/2020] [Indexed: 12/31/2022]
5
Phylogenetic analysis of protein sequences based on a novel k-mer natural vector method. Genomics 2018;111:1298-1305. [PMID: 30195069 DOI: 10.1016/j.ygeno.2018.08.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 08/19/2018] [Accepted: 08/27/2018] [Indexed: 11/22/2022]
6
He L, Li Y, He RL, Yau SST. A novel alignment-free vector method to cluster protein sequences. J Theor Biol 2017;427:41-52. [DOI: 10.1016/j.jtbi.2017.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/04/2017] [Accepted: 06/02/2017] [Indexed: 11/29/2022]
7
Li Y, Tian K, Yin C, He RL, Yau SST. Virus classification in 60-dimensional protein space. Mol Phylogenet Evol 2016;99:53-62. [PMID: 26988414 DOI: 10.1016/j.ympev.2016.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 01/24/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
8
Yang WF, Yu ZG, Anh V. Whole genome/proteome based phylogeny reconstruction for prokaryotes using higher order Markov model and chaos game representation. Mol Phylogenet Evol 2015;96:102-111. [PMID: 26724405 DOI: 10.1016/j.ympev.2015.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 01/18/2023]
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