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BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.
Syst Biol. 2012 Jan;61(1):170-3. doi: 10.1093/sysbio/syr100. Epub 2011 Oct 1.
Syst Biol. 2012.
PMID: 21963610
Free PMC article.
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space.
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP.
Ronquist F, et al. Among authors: ayres dl.
Syst Biol. 2012 May;61(3):539-42. doi: 10.1093/sysbio/sys029. Epub 2012 Feb 22.
Syst Biol. 2012.
PMID: 22357727
Free PMC article.
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Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10.
Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A.
Suchard MA, et al. Among authors: ayres dl.
Virus Evol. 2018 Jun 8;4(1):vey016. doi: 10.1093/ve/vey016. eCollection 2018 Jan.
Virus Evol. 2018.
PMID: 29942656
Free PMC article.
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Comparative morphology and evolution of the cnidosac in Cladobranchia (Gastropoda: Heterobranchia: Nudibranchia).
Goodheart JA, Bleidißel S, Schillo D, Strong EE, Ayres DL, Preisfeld A, Collins AG, Cummings MP, Wägele H.
Goodheart JA, et al. Among authors: ayres dl.
Front Zool. 2018 Nov 13;15:43. doi: 10.1186/s12983-018-0289-2. eCollection 2018.
Front Zool. 2018.
PMID: 30473719
Free PMC article.
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BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics.
Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA.
Ayres DL, et al.
Syst Biol. 2019 Nov 1;68(6):1052-1061. doi: 10.1093/sysbio/syz020.
Syst Biol. 2019.
PMID: 31034053
Free PMC article.
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High-Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE.
Baele G, Ayres DL, Rambaut A, Suchard MA, Lemey P.
Baele G, et al. Among authors: ayres dl.
Methods Mol Biol. 2019;1910:691-722. doi: 10.1007/978-1-4939-9074-0_23.
Methods Mol Biol. 2019.
PMID: 31278682
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Bayesian Phylogenetic Analysis on multi-core Compute Architectures: Implementation and evaluation of BEAGLE in RevBayes with MPI.
Smith K, Ayres D, Neumaier R, Worheide G, Hohna S.
Smith K, et al.
Syst Biol. 2024 Jan 29:syae005. doi: 10.1093/sysbio/syae005. Online ahead of print.
Syst Biol. 2024.
PMID: 38284268
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Assessing a model of Pacific Northwest harmful algal bloom transport as a decision-support tool.
Stone HB, Banas NS, MacCready P, Trainer VL, Ayres DL, Hunter MV.
Stone HB, et al. Among authors: ayres dl.
Harmful Algae. 2022 Nov;119:102334. doi: 10.1016/j.hal.2022.102334. Epub 2022 Oct 29.
Harmful Algae. 2022.
PMID: 36344195
Free article.
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