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Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7
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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6101584/ https://www.ncbi.nlm.nih.gov/pubmed/29718447 http://dx.doi.org/10.1093/sysbio/syy032 |
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author | Rambaut, Andrew Drummond, Alexei J Xie, Dong Baele, Guy Suchard, Marc A |
author_facet | Rambaut, Andrew Drummond, Alexei J Xie, Dong Baele, Guy Suchard, Marc A |
author_sort | Rambaut, Andrew |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6101584 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-61015842018-08-27 Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 Rambaut, Andrew Drummond, Alexei J Xie, Dong Baele, Guy Suchard, Marc A Syst Biol Software for Systematics and Evolution 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. Oxford University Press 2018-09 2018-04-27 /pmc/articles/PMC6101584/ /pubmed/29718447 http://dx.doi.org/10.1093/sysbio/syy032 Text en © The Author(s) 2018. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For Permissions, please email: journals.permissions@oup.com |
spellingShingle | Software for Systematics and Evolution Rambaut, Andrew Drummond, Alexei J Xie, Dong Baele, Guy Suchard, Marc A Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 |
title | Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 |
title_full | Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 |
title_fullStr | Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 |
title_full_unstemmed | Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 |
title_short | Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 |
title_sort | posterior summarization in bayesian phylogenetics using tracer 1.7 |
topic | Software for Systematics and Evolution |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6101584/ https://www.ncbi.nlm.nih.gov/pubmed/29718447 http://dx.doi.org/10.1093/sysbio/syy032 |
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