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For: Smith ML, Hahn MW. Phylogenetic inference using generative adversarial networks. Bioinformatics 2023;39:btad543. [PMID: 37669126 PMCID: PMC10500083 DOI: 10.1093/bioinformatics/btad543] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/07/2023]  Open
Number Cited by Other Article(s)
1
Salles MMA, Domingos FMCB. Towards the next generation of species delimitation methods: an overview of machine learning applications. Mol Phylogenet Evol 2025;210:108368. [PMID: 40348350 DOI: 10.1016/j.ympev.2025.108368] [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: 12/21/2023] [Revised: 02/25/2025] [Accepted: 05/04/2025] [Indexed: 05/14/2025]
2
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]
3
Nesterenko L, Blassel L, Veber P, Boussau B, Jacob L. Phyloformer: Fast, Accurate, and Versatile Phylogenetic Reconstruction with Deep Neural Networks. Mol Biol Evol 2025;42:msaf051. [PMID: 40066802 PMCID: PMC11965795 DOI: 10.1093/molbev/msaf051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 01/16/2025] [Accepted: 01/27/2025] [Indexed: 04/04/2025]  Open
4
Landis MJ, Thompson A. phyddle: software for exploring phylogenetic models with deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.08.06.606717. [PMID: 39149349 PMCID: PMC11326143 DOI: 10.1101/2024.08.06.606717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
5
Roa Lozano J, Duncan M, McKenna DD, Castoe TA, DeGiorgio M, Adams R. TraitTrainR: accelerating large-scale simulation under models of continuous trait evolution. BIOINFORMATICS ADVANCES 2024;5:vbae196. [PMID: 39758830 PMCID: PMC11696700 DOI: 10.1093/bioadv/vbae196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 11/08/2024] [Accepted: 12/05/2024] [Indexed: 01/07/2025]
6
Silvestro D, Latrille T, Salamin N. Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation. Syst Biol 2024;73:789-806. [PMID: 38916476 PMCID: PMC11639169 DOI: 10.1093/sysbio/syae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 05/21/2024] [Accepted: 06/24/2024] [Indexed: 06/26/2024]  Open
7
Bernardini G, van Iersel L, Julien E, Stougie L. Inferring phylogenetic networks from multifurcating trees via cherry picking and machine learning. Mol Phylogenet Evol 2024;199:108137. [PMID: 39029549 DOI: 10.1016/j.ympev.2024.108137] [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: 11/18/2023] [Revised: 02/19/2024] [Accepted: 06/29/2024] [Indexed: 07/21/2024]
8
Li Z, Hu Y, Song Y, Li D, Yang X, Zhang L, Li T, Wang H. Diversity, Distribution and Structural Prediction of the Pathogenic Bacterial Effectors EspN and EspS. Genes (Basel) 2024;15:1250. [PMID: 39457374 PMCID: PMC11507257 DOI: 10.3390/genes15101250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2024] [Revised: 09/20/2024] [Accepted: 09/23/2024] [Indexed: 10/28/2024]  Open
9
He Y, Mulqueeney JM, Watt EC, Salili-James A, Barber NS, Camaiti M, Hunt ESE, Kippax-Chui O, Knapp A, Lanzetti A, Rangel-de Lázaro G, McMinn JK, Minus J, Mohan AV, Roberts LE, Adhami D, Grisan E, Gu Q, Herridge V, Poon STS, West T, Goswami A. Opportunities and Challenges in Applying AI to Evolutionary Morphology. Integr Org Biol 2024;6:obae036. [PMID: 40433986 PMCID: PMC12082097 DOI: 10.1093/iob/obae036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 08/07/2024] [Accepted: 09/20/2024] [Indexed: 05/29/2025]  Open
10
Li X, Zhou T, Feng X, Yau ST, Yau SST. Exploring geometry of genome space via Grassmann manifolds. Innovation (N Y) 2024;5:100677. [PMID: 39206218 PMCID: PMC11350263 DOI: 10.1016/j.xinn.2024.100677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 07/18/2024] [Indexed: 09/04/2024]  Open
11
Mello B, Schrago CG. Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock. Genome Biol Evol 2024;16:evae199. [PMID: 39332907 PMCID: PMC11430275 DOI: 10.1093/gbe/evae199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2024] [Indexed: 09/29/2024]  Open
12
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]
13
Leuchtenberger AF, von Haeseler A. Learning From an Artificial Neural Network in Phylogenetics. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:278-288. [PMID: 38198267 DOI: 10.1109/tcbb.2024.3352268] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
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