2018 | ANDREW RAMBAUT1, ALEXEI J. DRUMMOND2,3, DONG XIE2,3, GUY BAELE4, AND MARC A. SUCHARD5,6
Tracer 1.7 is a software package for visualizing and analyzing MCMC trace files generated from Bayesian phylogenetic inference. It provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, and conditional posterior distribution summary. Tracer is open-source and available at http://beast.community/tracer. It works with sample output from BEAST, BEAST2, LAMARC, Migrate, MrBayes, RevBayes, and other MCMC programs.
Tracer examines posterior samples from all available parameters and presents statistical summaries and visualizations. It can analyze a single trace or combine samples from multiple files. The effective sample size (ESS) is a key statistic for assessing the number of effectively independent draws from the posterior distribution. Color coding helps identify potential MCMC mixing problems.
Tracer allows users to compare multiple parameters side-by-side or overlay their visualizations. It generates four display panels for the selected parameters: Estimates, Marginal density, Joint-marginal, and Trace. Estimates report summary statistics such as the sample mean, standard deviation, highest posterior density interval, and ESS. Marginal density plots include kernel density estimates, histograms, and violin plots for continuous parameters and frequency plots for categorical or integer parameters. Joint-marginal visualization appears after selecting two or more parameters and depends on the parameter types. Trace constructs line plots connecting the sequential samples of one or more selected parameters against state or generation number.
Tracer also provides visualizations of conditional posterior distributions. Selecting one continuous and one integer or categorical parameter generates side-by-side violin or boxplots under the Joint-Marginal panel. These plots present the continuous parameter distribution conditioned on the unique integer or categorical values. Tracer reconstructs the demographic history of RABV by drawing the effective population sizes over time. RABV has successfully established itself in North American bat species, with its effective population size rising steadily throughout recent centuries. Following a rapid decline at the end of last century, we observe a recent sharp increase in size.
Tracer is open-source under the GNU lesser general public license and available in both source code and executable forms. It provides tutorials covering basic to advanced usage of Tracer to summarize posteriors under a variety of phylogenetic models using BEAST and diagnose MCMC chain convergence. Tracer requires Java version 1.6 or greater.Tracer 1.7 is a software package for visualizing and analyzing MCMC trace files generated from Bayesian phylogenetic inference. It provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, and conditional posterior distribution summary. Tracer is open-source and available at http://beast.community/tracer. It works with sample output from BEAST, BEAST2, LAMARC, Migrate, MrBayes, RevBayes, and other MCMC programs.
Tracer examines posterior samples from all available parameters and presents statistical summaries and visualizations. It can analyze a single trace or combine samples from multiple files. The effective sample size (ESS) is a key statistic for assessing the number of effectively independent draws from the posterior distribution. Color coding helps identify potential MCMC mixing problems.
Tracer allows users to compare multiple parameters side-by-side or overlay their visualizations. It generates four display panels for the selected parameters: Estimates, Marginal density, Joint-marginal, and Trace. Estimates report summary statistics such as the sample mean, standard deviation, highest posterior density interval, and ESS. Marginal density plots include kernel density estimates, histograms, and violin plots for continuous parameters and frequency plots for categorical or integer parameters. Joint-marginal visualization appears after selecting two or more parameters and depends on the parameter types. Trace constructs line plots connecting the sequential samples of one or more selected parameters against state or generation number.
Tracer also provides visualizations of conditional posterior distributions. Selecting one continuous and one integer or categorical parameter generates side-by-side violin or boxplots under the Joint-Marginal panel. These plots present the continuous parameter distribution conditioned on the unique integer or categorical values. Tracer reconstructs the demographic history of RABV by drawing the effective population sizes over time. RABV has successfully established itself in North American bat species, with its effective population size rising steadily throughout recent centuries. Following a rapid decline at the end of last century, we observe a recent sharp increase in size.
Tracer is open-source under the GNU lesser general public license and available in both source code and executable forms. It provides tutorials covering basic to advanced usage of Tracer to summarize posteriors under a variety of phylogenetic models using BEAST and diagnose MCMC chain convergence. Tracer requires Java version 1.6 or greater.