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references.bib
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@article{metropolis53,
author={Nicholas Metropolis and Arianna W. Rosenbluth and Marshall N. Rosenbluth and Augusta H. Teller},
title={Equation of state calculations by fast computing machines},
journal={{J. Chem. Phys.}},
volume={21},
issue={6},
pages={1087--1092},
year={1953}
}
@book{beastbook,
Author = {Alexei J. Drummond and Remco R. Bouckaert},
Publisher = {Cambridge University Press},
Title = {Bayesian evolutionary analysis with {B}{E}{A}{S}{T}},
address={Cambridge},
Year = {2015}
}
@article{beast,
Author = {Bouckaert, Remco R. 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, A
lexei J},
Date-Added = {2014-05-21 03:24:22 +0000},
Date-Modified = {2015-07-02 08:20:30 +0000},
Doi = {10.1371/journal.pcbi.1003537},
Journal = {PLoS Comput Biol},
Journal-Full = {PLoS computational biology},
Month = {Apr},
Number = {4},
Pages = {e1003537},
Pmc = {PMC3985171},
Pmid = {24722319},
Pst = {epublish},
Title = {{BEAST 2}: a software platform for {B}ayesian evolutionary analysis},
Volume = {10},
Year = {2014},
Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pcbi.1003537}
}
@article{bryant2012inferring,
title={Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis},
author={Bryant, David and Bouckaert, Remco and Felsenstein, Joseph and Rosenberg, Noah A and RoyChoudhury, Arindam},
journal={Molecular biology and evolution},
volume={29},
number={8},
pages={1917--1932},
year={2012},
publisher={Oxford University Press}
}
@article{vaughan2013stochastic,
title={A stochastic simulator of birth--death master equations with application to phylodynamics},
author={Vaughan, Timothy G and Drummond, Alexei J},
journal={Molecular biology and evolution},
volume={30},
number={6},
pages={1480--1493},
year={2013},
publisher={Oxford University Press}
}
@article{bouckaert2019beast,
title={BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis},
author={Bouckaert, Remco and Vaughan, Timothy G and Barido-Sottani, Jo{\"e}lle and Duch{\^e}ne, Sebasti{\'a}n and Fourment, Mathieu and Gavryushkina, Alexandra and Heled, Joseph and Jones, Graham and K{\"u}hnert, Denise and De Maio, Nicola and others},
journal={PLoS computational biology},
volume={15},
number={4},
pages={e1006650},
year={2019},
publisher={Public Library of Science}
}
@article{lynch2010evolution,
title={Evolution of the mutation rate},
author={Lynch, Michael},
journal={TRENDS in Genetics},
volume={26},
number={8},
pages={345--352},
year={2010},
publisher={Elsevier}
}
@article{cuevas2015extremely,
title={Extremely high mutation rate of HIV-1 in vivo},
author={Cuevas, Jos{\'e} M and Geller, Ron and Garijo, Raquel and L{\'o}pez-Aldeguer, Jos{\'e} and Sanju{\'a}n, Rafael},
journal={PLoS biology},
volume={13},
number={9},
pages={e1002251},
year={2015},
publisher={Public Library of Science}
}
@article{talts2018validating,
title={Validating Bayesian inference algorithms with simulation-based calibration},
author={Talts, Sean and Betancourt, Michael and Simpson, Daniel and Vehtari, Aki and Gelman, Andrew},
journal={arXiv preprint arXiv:1804.06788},
year={2018}
}
@article{inla,
title={Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations},
author={Rue, H{\aa}vard and Martino, Sara and Chopin, Nicolas},
journal={Journal of the royal statistical society: Series b (statistical methodology)},
volume={71},
number={2},
pages={319--392},
year={2009},
publisher={Wiley Online Library}
}
@article{Birnbaum1951,
title={One-sided confidence contours for probability distribution functions},
author={Birnbaum, ZW and Tingey, Fred H},
journal={The Annals of Mathematical Statistics},
pages={592--596},
year={1951},
publisher={JSTOR}
}