Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7

Systematic Biology - Tập 67 Số 5 - Trang 901-904 - 2018
Andrew Rambaut1, Alexei J. Drummond2,3, Dong Xie2,3, Guy Baele4, Marc A. Suchard5,6
1Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King's Buildings, Edinburgh, EH9 3FL, UK
2Centre for Computational Evolution, University of Auckland, 303/38 Princes St, Auckland, 1010, NZ
3Department of Computer Science, University of Auckland, 303/38 Princes St, Auckland, 1010, NZ
4Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Herestraat 49, 3000 Leuven, Belgium
5Department of Biostatistics, University of California, Los Angeles, 650 Charles E. Young Dr., Los Angeles, CA 90095, USA
6Department of Human Genetics, University of California, Los Angeles, 695 Charles E. Young Dr., Los Angeles, CA 90095, USA

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Tài liệu tham khảo

Beerli, 2006, Comparison of Bayesian and maximum-likelihood inference of population genetic parameters., Bioinformatics, 22, 341, 10.1093/bioinformatics/bti803

Bouckaert, 2014, BEAST 2: a software platform for Bayesian evolutionary analysis., PLoS Comp. Biol., 10, e1003537, 10.1371/journal.pcbi.1003537

Drummond,, 2002, Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data., Genetics, 161, 1307, 10.1093/genetics/161.3.1307

Drummond,, 2005, Bayesian coalescent inference of past population dynamics from molecular sequences., Mol. Biol. Evol., 22, 1185, 10.1093/molbev/msi103

Drummond, 2012, Bayesian phylogenetics with BEAUti and the BEAST 1.7., Mol. Biol. Evol., 29, 1969, 10.1093/molbev/mss075

Faria,, 2013, Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraint., Philos. Trans. R. Soc. Lon. B, 368, 20120196, 10.1098/rstb.2012.0196

Gelman, 1992, Inference from iterative simulation using multiple sequences., Stat. Sci., 7, 457, 10.1214/ss/1177011136

Gill,, 2013, Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci., Mol. Biol. Evol., 30, 713, 10.1093/molbev/mss265

Heled, 2008, Bayesian inference of population size history from multiple loci., BMC Evol. Biol., 8, 289, 10.1186/1471-2148-8-289

Höhna, 2016, RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language., Syst. Biol., 65, 726, 10.1093/sysbio/syw021

Kuhner, 2006, LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters., Bioinformatics, 22, 768, 10.1093/bioinformatics/btk051

Lemey, 2009, Bayesian phylogeography finds its roots., PLoS Comp. Biol., 5, e1000520, 10.1371/journal.pcbi.1000520

Li, 2012, Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics., Mol. Biol. Evol., 29, 751, 10.1093/molbev/msr232

Mau, 1999, Bayesian phylogenetic inference via Markov chain Monte Carlo methods., Biometrics, 55, 1, 10.1111/j.0006-341X.1999.00001.x

Minin, 2008, Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics., Mol. Biol. Evol., 25, 1459, 10.1093/molbev/msn090

Murdoch, 1996, A graphical display of large correlation matrices., Am. Stat., 50, 178, 10.1080/00031305.1996.10474371

Nylander, 2007, AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics., Bioinformatics, 24, 581, 10.1093/bioinformatics/btm388

Plummer, 2006, CODA: convergence diagnosis and output analysis for MCMC., R News, 6, 7

Rannala, 1996, Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference., J. Mol. Evol., 43, 304, 10.1007/BF02338839

Ronquist, 2012, MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space., Syst. Biol., 61, 539, 10.1093/sysbio/sys029

Streicker, 2010, Host phylogeny constrains cross-species emergence and establishment of rabies virus in bats., Science, 329, 676, 10.1126/science.1188836

Warren, 2017, RWTY (R We There Yet): an R package for examining convergence of Bayesian phylogenetic analyses., Mol. Biol. Evol., 34, 1016