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Syst Biol. 2018 Sep 1;67(5):901-904. doi: 10.1093/sysbio/syy032.

Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7.

Author information

1
Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, King's Buildings, Edinburgh, EH9 3FL, UK.
2
Department of Computer Science, University of Auckland, 303/38 Princes St, Auckland, 1010, NZ.
3
Centre for Computational Evolution, University of Auckland, 303/38 Princes St, Auckland, 1010, NZ.
4
Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Herestraat 49, 3000 Leuven, Belgium.
5
Department of Human Genetics, University of California, Los Angeles, 695 Charles E. Young Dr., Los Angeles, CA 90095, USA.
6
Department of Biostatistics, University of California, Los Angeles, 650 Charles E. Young Dr., Los Angeles, CA 90095, USA.

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.

PMID:
29718447
PMCID:
PMC6101584
DOI:
10.1093/sysbio/syy032
[Indexed for MEDLINE]
Free PMC Article

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