master-refs.bib

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@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{Bouckaert2019,
  title = {BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis},
  volume = {15},
  number = {4},
  journal = {PLOS Computational Biology},
  author = {Bouckaert, Remco and Vaughan, Timothy G. and Barido-Sottani, Joëlle and Duchêne, Sebastián and Fourment, Mathieu and Gavryushkina, Alexandra and Heled, Joseph and Jones, Graham and Kühnert, Denise and Maio, Nicola De and Matschiner, Michael and Mendes, Fábio K. and Müller, Nicola F. and Ogilvie, Huw A. and Plessis, Louis du and Popinga, Alex and Rambaut, Andrew and Rasmussen, David and Siveroni, Igor and Suchard, Marc A. and Wu, Chieh-Hsi and Xie, Dong and Zhang, Chi and Stadler, Tanja and Drummond, Alexei J.},
  year = {2019}
}