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For: Scheffler K, Murrell B, Kosakovsky Pond SL. On the validity of evolutionary models with site-specific parameters. PLoS One 2014;9:e94534. [PMID: 24722425 PMCID: PMC3983186 DOI: 10.1371/journal.pone.0094534] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 03/17/2014] [Indexed: 11/28/2022]  Open
Number Cited by Other Article(s)
1
Martin DP, Weaver S, Tegally H, San JE, Shank SD, Wilkinson E, Lucaci AG, Giandhari J, Naidoo S, Pillay Y, Singh L, Lessells RJ, Gupta RK, Wertheim JO, Nekturenko A, Murrell B, Harkins GW, Lemey P, MacLean OA, Robertson DL, de Oliveira T, Kosakovsky Pond SL. The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages. Cell 2021;184:5189-5200.e7. [PMID: 34537136 PMCID: PMC8421097 DOI: 10.1016/j.cell.2021.09.003] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/05/2021] [Accepted: 09/01/2021] [Indexed: 12/18/2022]
2
Kosakovsky Pond SL, Wisotsky SR, Escalante A, Magalis BR, Weaver S. Contrast-FEL-A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches. Mol Biol Evol 2021;38:1184-1198. [PMID: 33064823 PMCID: PMC7947784 DOI: 10.1093/molbev/msaa263] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
3
Puller V, Sagulenko P, Neher RA. Efficient inference, potential, and limitations of site-specific substitution models. Virus Evol 2020;6:veaa066. [PMID: 33343922 PMCID: PMC7733610 DOI: 10.1093/ve/veaa066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
4
Spielman SJ, Kosakovsky Pond SL. Relative Evolutionary Rates in Proteins Are Largely Insensitive to the Substitution Model. Mol Biol Evol 2018;35:2307-2317. [PMID: 29924340 PMCID: PMC6107055 DOI: 10.1093/molbev/msy127] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
5
Spielman SJ, Kosakovsky Pond SL. Relative evolutionary rate inference in HyPhy with LEISR. PeerJ 2018;6:e4339. [PMID: 29423346 PMCID: PMC5804317 DOI: 10.7717/peerj.4339] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 01/18/2018] [Indexed: 01/10/2023]  Open
6
Spielman SJ, Wilke CO. Extensively Parameterized Mutation-Selection Models Reliably Capture Site-Specific Selective Constraint. Mol Biol Evol 2016;33:2990-3002. [PMID: 27512115 DOI: 10.1093/molbev/msw171] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
7
Mingrone J, Susko E, Bielawski J. Smoothed Bootstrap Aggregation for Assessing Selection Pressure at Amino Acid Sites. Mol Biol Evol 2016;33:2976-2989. [PMID: 27486222 DOI: 10.1093/molbev/msw160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
8
Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL. Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Mol Biol Evol 2015;32:1342-53. [PMID: 25697341 DOI: 10.1093/molbev/msv022] [Citation(s) in RCA: 501] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
9
Wertheim JO, Murrell B, Smith MD, Kosakovsky Pond SL, Scheffler K. RELAX: detecting relaxed selection in a phylogenetic framework. Mol Biol Evol 2014;32:820-32. [PMID: 25540451 DOI: 10.1093/molbev/msu400] [Citation(s) in RCA: 464] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
10
Wertheim JO, Smith MD, Smith DM, Scheffler K, Kosakovsky Pond SL. Evolutionary origins of human herpes simplex viruses 1 and 2. Mol Biol Evol 2014;31:2356-64. [PMID: 24916030 PMCID: PMC4137711 DOI: 10.1093/molbev/msu185] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
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