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Pandemic-scale phylogenetics.
Ye C, Thornlow B, Kramer A, McBroome J, Hinrichs A, Corbett-Detig R, Turakhia Y. Ye C, et al. bioRxiv [Preprint]. 2021 Dec 6:2021.12.03.470766. doi: 10.1101/2021.12.03.470766. bioRxiv. 2021. PMID: 34927180 Free PMC article. Preprint.
Stability of SARS-CoV-2 phylogenies.
Turakhia Y, De Maio N, Thornlow B, Gozashti L, Lanfear R, Walker CR, Hinrichs AS, Fernandes JD, Borges R, Slodkowicz G, Weilguny L, Haussler D, Goldman N, Corbett-Detig R. Turakhia Y, et al. PLoS Genet. 2020 Nov 18;16(11):e1009175. doi: 10.1371/journal.pgen.1009175. eCollection 2020 Nov. PLoS Genet. 2020. PMID: 33206635 Free PMC article.
Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape.
Turakhia Y, Thornlow B, Hinrichs A, McBroome J, Ayala N, Ye C, Smith K, De Maio N, Haussler D, Lanfear R, Corbett-Detig R. Turakhia Y, et al. Nature. 2022 Sep;609(7929):994-997. doi: 10.1038/s41586-022-05189-9. Epub 2022 Aug 11. Nature. 2022. PMID: 35952714 Free PMC article.
Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Approaches.
Thornlow B, Kramer A, Ye C, De Maio N, McBroome J, Hinrichs AS, Lanfear R, Turakhia Y, Corbett-Detig R. Thornlow B, et al. bioRxiv [Preprint]. 2022 May 18:2021.12.02.471004. doi: 10.1101/2021.12.02.471004. bioRxiv. 2022. Update in: Syst Biol. 2023 Nov 1;72(5):1039-1051. doi: 10.1093/sysbio/syad031 PMID: 35611334 Free PMC article. Updated. Preprint.
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