Abstract
Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular sequence data. Visualizing and analyzing the MCMC-generated samples from the posterior distribution is a key step in any non-trivial Bayesian inference. We present the software package Tracer (version 1.7) for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more. Tracer is open-source and available at http://beast.community/tracer.
Highlights
Estimates: Reports common summary statistics such as the sample mean, standard deviation, highest posterior density interval, and effective sample size (ESS)
Visualizing, tabulating, and marginalizing these samples are critical for approximating the posterior quantities of interest that one reports as the outcome of a Bayesian phylogenetic analysis
We have developed the Tracer software package to process Markov chain Monte Carlo (MCMC) trace files containing parameter samples and to interactively explore the high-dimensional posterior distribution
Summary
Citation for published version: Rambaut, A, Drummond, AJ, Xie, D, Baele, G & Suchard, MA 2018, 'Posterior summarisation in Bayesian phylogenetics using Tracer 1.7', Systematic biology, vol 67, pp. We present the software package Tracer (version 1.7) for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference. MCMC approaches generate samples of model parameter values—including the phylogenetic tree—drawn from their posterior distribution given molecular sequence data and a selection of evolutionary models. Visualizing, tabulating, and marginalizing these samples are critical for approximating the posterior quantities of interest that one reports as the outcome of a Bayesian phylogenetic analysis To facilitate this task, we have developed the Tracer (version 1.7) software package to process MCMC trace files containing parameter samples and to interactively explore the high-dimensional posterior distribution. Tracer works automatically with sample output from BEAST (Drummond et al 2012), BEAST2 (Bouckaert et al 2014), LAMARC (Kuhner 2006), Migrate (Beerli 2006), MrBayes (Ronquist et al 2012), RevBayes (Höhna et al 2016), and possibly other MCMC programs from other domains
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