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For: Molloy EK, Warnow T. TreeMerge: a new method for improving the scalability of species tree estimation methods. Bioinformatics 2019;35:i417-i426. [PMID: 31510668 PMCID: PMC6612878 DOI: 10.1093/bioinformatics/btz344] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
Number Cited by Other Article(s)
1
He J, Li M, Wu H, Cheng J, Xie L. Unraveling the Ancient Introgression History of Xanthoceras (Sapindaceae): Insights from Phylogenomic Analysis. Int J Mol Sci 2025;26:1581. [PMID: 40004047 PMCID: PMC11855356 DOI: 10.3390/ijms26041581] [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: 01/07/2025] [Revised: 02/07/2025] [Accepted: 02/10/2025] [Indexed: 02/27/2025]  Open
2
Piñeiro C, Pichel JC. Efficient phylogenetic tree inference for massive taxonomic datasets: harnessing the power of a server to analyze 1 million taxa. Gigascience 2024;13:giae055. [PMID: 39115958 PMCID: PMC11308190 DOI: 10.1093/gigascience/giae055] [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: 10/23/2023] [Revised: 04/17/2024] [Accepted: 07/11/2024] [Indexed: 08/10/2024]  Open
3
Wang Z, Sun J, Gao Y, Xue Y, Zhang Y, Li K, Zhang W, Zhang C, Zu J, Zhang L. Fusang: a framework for phylogenetic tree inference via deep learning. Nucleic Acids Res 2023;51:10909-10923. [PMID: 37819036 PMCID: PMC10639059 DOI: 10.1093/nar/gkad805] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 08/17/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023]  Open
4
Aizenbud Y, Jaffe A, Wang M, Hu A, Amsel N, Nadler B, Chang JT, Kluger Y. Spectral top-down recovery of latent tree models. INFORMATION AND INFERENCE : A JOURNAL OF THE IMA 2023;12:iaad032. [PMID: 37593361 PMCID: PMC10431953 DOI: 10.1093/imaiai/iaad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/24/2023] [Accepted: 06/24/2023] [Indexed: 08/19/2023]
5
Zaharias P, Warnow T. Recent progress on methods for estimating and updating large phylogenies. Philos Trans R Soc Lond B Biol Sci 2022;377:20210244. [PMID: 35989607 PMCID: PMC9393559 DOI: 10.1098/rstb.2021.0244] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/07/2022] [Indexed: 12/20/2022]  Open
6
Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation. ALGORITHMS 2021. [DOI: 10.3390/a14050148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
7
Matsumoto H, Mimori T, Fukunaga T. Novel metric for hyperbolic phylogenetic tree embeddings. Biol Methods Protoc 2021;6:bpab006. [PMID: 33928190 PMCID: PMC8058397 DOI: 10.1093/biomethods/bpab006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 01/09/2023]  Open
8
Warnow T, Mirarab S. Multiple Sequence Alignment for Large Heterogeneous Datasets Using SATé, PASTA, and UPP. Methods Mol Biol 2021;2231:99-119. [PMID: 33289889 DOI: 10.1007/978-1-0716-1036-7_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
9
Le T, Sy A, Molloy EK, Zhang Q, Rao S, Warnow T. Using Constrained-INC for Large-Scale Gene Tree and Species Tree Estimation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:2-15. [PMID: 32750844 DOI: 10.1109/tcbb.2020.2990867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
10
Smirnov V, Warnow T. Phylogeny Estimation Given Sequence Length Heterogeneity. Syst Biol 2020;70:268-282. [PMID: 32692823 PMCID: PMC7875441 DOI: 10.1093/sysbio/syaa058] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/21/2022]  Open
11
Smirnov V, Warnow T. Unblended disjoint tree merging using GTM improves species tree estimation. BMC Genomics 2020;21:235. [PMID: 32299343 PMCID: PMC7161100 DOI: 10.1186/s12864-020-6605-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
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