master-refs.bib

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@STRING{AHG = {Annals of Human Genetics}}

@STRING{AJHG = {American Journal of Human Genetics}}

@STRING{ARB = {Annual Review of Biochemistry}}

@STRING{ARCB = {Annual Review of Cell Biology}}

@STRING{BI = {Bioinformatics}}

@STRING{BIOGEN = {Biochemical Genetics}}

@STRING{BJLS = {Biological Journal of the Linnean Society}}

@STRING{BMB = {Bulletin of Mathematical Biology}}

@STRING{BMCBI = {BMC Bioinformatics}}

@STRING{CABIOS = {Computer Applications in the Biosciences}}

@STRING{CACM = {Communications of the ACM}}

@STRING{CELL = {Cell}}

@STRING{COCB = {Current Opinion in Cell Biology}}

@STRING{COGD = {Current Opinion in Genetics and Development}}

@STRING{ComputChem = {Computers and Chemistry}}

@STRING{COSB = {Current Opinion in Structural Biology}}

@STRING{CSHSQB = {Cold Spring Harbor Symposia Quantitative Biology}}

@STRING{EMBO = {EMBO Journal}}

@STRING{EVO = {Evolution}}

@STRING{GB = {Genome Biology}}

@STRING{GEN = {Genetics}}

@STRING{GR = {Genome Research}}

@STRING{JBSD = {Journal of Biomolecular Structure and Dynamics}}

@STRING{JCB = {Journal of Computational Biology}}

@STRING{JMB = {Journal of Molecular Biology}}

@STRING{JME = {Journal of Molecular Evolution}}

@STRING{JRSS = {Journal of the Royal Statistical Society, B}}

@STRING{JTB = {Journal of Theoretical Biology}}

@STRING{MBE = {Molecular Biology and Evolution}}

@STRING{MBIO = {Mathematical Biosciences}}

@STRING{MCB = {Molecular Cell Biology}}

@STRING{ME = {Methods in Enzymology}}

@STRING{MPE = {Molecular Phylogenetics and Evolution}}

@STRING{NAR = {Nucleic Acids Research}}

@STRING{Nature = {Nature}}

@STRING{NB = {Nature Biotechnology}}

@STRING{NC = {Neural Computation}}

@STRING{NG = {Nature Genetics}}

@STRING{NNB = {Nature New Biology}}

@STRING{PE = {Protein Engineering}}

@STRING{PHTRANSRB = {Philosophical Transactions of the Royal Society B}}

@STRING{PLOSCOMPBIO = {PLoS Computational Biology}}

@STRING{PNAS = {Proceedings of the National Academy of Sciences, USA}}

@STRING{PROCROYB = {Proceedings of the Royal Society B}}

@STRING{PROT = {Proteins}}

@STRING{PROTSCI = {Protein Science}}

@STRING{Science = {Science}}

@STRING{S = Science}

@STRING{SIAM = {SIAM Journal of Applied Mathematics}}

@STRING{SYSB = {Systematic Biology}}

@STRING{SZ = {Systematic Zoology}}

@STRING{TIBTECH = {Trends in Biotechnology}}

@STRING{TIGS = {Trends in Genetics}}

@article{Bouckaert2014,
abstract = {We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.},
author = {Bouckaert, Remco and Heled, Joseph and K{\"{u}}hnert, Denise and Vaughan, Tim and Wu, Chieh-Hsi and Xie, Dong and Suchard, Marc A and Rambaut, Andrew and Drummond, Alexei J},
doi = {10.1371/journal.pcbi.1003537},
file = {:Users/nicmuell/Library/Application Support/Mendeley Desktop/Downloaded/Bouckaert et al. - 2014 - BEAST 2 a software platform for Bayesian evolutionary analysis.pdf:pdf},
issn = {1553-7358},
journal = {PLoS computational biology},
mendeley-groups = {Methods,SkylineTutorial},
month = {apr},
number = {4},
pages = {e1003537},
pmid = {24722319},
publisher = {Public Library of Science},
title = {BEAST 2: a software platform for Bayesian evolutionary analysis.},
url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003537},
volume = {10},
year = {2014}
}

@BOOK{BEAST2book2014,
  title = {Bayesian evolutionary analysis with {BEAST} 2},
  publisher = {Cambridge University Press},
  year = {2014},
  author = {Alexei J. Drummond and Remco R. Bouckaert}
}

@article{hugall2007calibration,
	title={Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1},
	author={Hugall, Andrew F and Foster, Ralph and Lee, Michael SY},
	journal={Systematic biology},
	volume={56},
	number={4},
	pages={543--563},
	year={2007},
	publisher={Oxford University Press}
}

@article{berling2025accurate,
	title={Accurate Bayesian phylogenetic point estimation using a tree distribution parameterized by clade probabilities},
	author={Berling, Lars and Klawitter, Jonathan and Bouckaert, Remco and Xie, Dong and Gavryushkin, Alex and Drummond, Alexei J},
	journal={PLOS Computational Biology},
	volume={21},
	number={2},
	pages={e1012789},
	year={2025},
	publisher={Public Library of Science San Francisco, CA USA}
}


@article{zrzavy2004phylogeny,
	title={Phylogeny of recent Canidae (Mammalia, Carnivora): relative reliability and utility of morphological and molecular datasets},
	author={Zrzav{\`y}, Jan and {\v{R}}I{\v{c}}{\'a}nkov{\'a}, V{\v{e}}ra},
	journal={Zoologica Scripta},
	volume={33},
	number={4},
	pages={311--333},
	year={2004},
	publisher={Wiley Online Library}
}

@article{heath2014fossilized,
	title={The fossilized birth--death process for coherent calibration of divergence-time estimates},
	author={Heath, Tracy A and Huelsenbeck, John P and Stadler, Tanja},
	journal={Proceedings of the National Academy of Sciences},
	volume={111},
	number={29},
	pages={E2957--E2966},
	year={2014},
	publisher={National Academy of Sciences}
}

@article{gavryushkina2014bayesian,
	title={Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration},
	author={Gavryushkina, Alexandra and Welch, David and Stadler, Tanja and Drummond, Alexei J},
	journal={PLoS computational biology},
	volume={10},
	number={12},
	pages={e1003919},
	year={2014},
	publisher={Public Library of Science San Francisco, USA}
}

@article{lindblad2005genome,
	title={Genome sequence, comparative analysis and haplotype structure of the domestic dog},
	author={Lindblad-Toh, Kerstin and Wade, Claire M and Mikkelsen, Tarjei S and Karlsson, Elinor K and Jaffe, David B and Kamal, Michael and Clamp, Michele and Chang, Jean L and Kulbokas III, Edward J and Zody, Michael C and others},
	journal={Nature},
	volume={438},
	number={7069},
	pages={803--819},
	year={2005},
	publisher={Nature Publishing Group UK London}
}

@article{douglas2022starbeast3,
	title={StarBeast3: adaptive parallelized Bayesian inference under the multispecies coalescent},
	author={Douglas, Jordan and Jim{\'e}nez-Silva, Cinthy L and Bouckaert, Remco},
	journal={Systematic Biology},
	volume={71},
	number={4},
	pages={901--916},
	year={2022},
	publisher={Oxford University Press}
}