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For: Burgstaller-Muehlbacher S, Crotty SM, Schmidt HA, Reden F, Drucks T, von Haeseler A. ModelRevelator: Fast phylogenetic model estimation via deep learning. Mol Phylogenet Evol 2023;188:107905. [PMID: 37595933 DOI: 10.1016/j.ympev.2023.107905] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 08/12/2023] [Indexed: 08/20/2023]
Number Cited by Other Article(s)
1
Zhu Y, Li Y, Li C, Shen XX, Zhou X. A critical evaluation of deep-learning based phylogenetic inference programs using simulated datasets. J Genet Genomics 2025;52:714-717. [PMID: 39824436 DOI: 10.1016/j.jgg.2025.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2024] [Revised: 01/08/2025] [Accepted: 01/09/2025] [Indexed: 01/20/2025]
2
Tinh NH, Vinh LS. An efficient deep learning method for amino acid substitution model selection. J Evol Biol 2025;38:129-139. [PMID: 39548851 DOI: 10.1093/jeb/voae141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 10/03/2024] [Accepted: 11/13/2024] [Indexed: 11/18/2024]
3
Kulikov N, Derakhshandeh F, Mayer C. Machine learning can be as good as maximum likelihood when reconstructing phylogenetic trees and determining the best evolutionary model on four taxon alignments. Mol Phylogenet Evol 2024;200:108181. [PMID: 39209046 DOI: 10.1016/j.ympev.2024.108181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 07/15/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
4
Mo YK, Hahn MW, Smith ML. Applications of machine learning in phylogenetics. Mol Phylogenet Evol 2024;196:108066. [PMID: 38565358 DOI: 10.1016/j.ympev.2024.108066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/16/2024] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
5
Ecker N, Huchon D, Mansour Y, Mayrose I, Pupko T. A machine-learning-based alternative to phylogenetic bootstrap. Bioinformatics 2024;40:i208-i217. [PMID: 38940166 PMCID: PMC11211842 DOI: 10.1093/bioinformatics/btae255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]  Open
6
Zou Y, Zhang Z, Zeng Y, Hu H, Hao Y, Huang S, Li B. Common Methods for Phylogenetic Tree Construction and Their Implementation in R. Bioengineering (Basel) 2024;11:480. [PMID: 38790347 PMCID: PMC11117635 DOI: 10.3390/bioengineering11050480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]  Open
7
Williams TA, Davin AA, Szánthó LL, Stamatakis A, Wahl NA, Woodcroft BJ, Soo RM, Eme L, Sheridan PO, Gubry-Rangin C, Spang A, Hugenholtz P, Szöllősi GJ. Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution. THE ISME JOURNAL 2024;18:wrae129. [PMID: 39001714 PMCID: PMC11293204 DOI: 10.1093/ismejo/wrae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/01/2024] [Accepted: 07/12/2024] [Indexed: 07/15/2024]
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