Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7
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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