RWTY (R We There Yet): An R package for examining convergence of Bayesian phylogenetic analyses

Dan L. Warren, Anthony J. Geneva, Robert Lanfear, Michael Rosenberg

Research output: Contribution to journalArticle

56 Citations (Scopus)

Abstract

Bayesian inference using Markov chain Monte Carlo (MCMC) has become one of the primary methods used to infer phylogenies from sequence data. Assessing convergence is a crucial component of these analyses, as it establishes the reliability of the posterior distribution estimates of the tree topology and model parameters sampled from the MCMC. Numerous tests and visualizations have been developed for this purpose, but many of the most popular methods are implemented in ways that make them inconvenient to use for large data sets. RWTY is an R package that implements established and new methods for diagnosing phylogenetic MCMC convergence in a single convenient interface.

Original languageEnglish (US)
Pages (from-to)1016-1020
Number of pages5
JournalMolecular Biology and Evolution
Volume34
Issue number4
DOIs
StatePublished - Apr 1 2017

Fingerprint

Markov Chains
Bayes Theorem
Markov chain
phylogenetics
phylogeny
Phylogeny
topology
visualization
methodology
method
testing

Keywords

  • Convergence
  • MCMC
  • MCMC
  • Phylogenetics
  • Stationarity
  • Topology

ASJC Scopus subject areas

  • Medicine(all)
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

RWTY (R We There Yet) : An R package for examining convergence of Bayesian phylogenetic analyses. / Warren, Dan L.; Geneva, Anthony J.; Lanfear, Robert; Rosenberg, Michael.

In: Molecular Biology and Evolution, Vol. 34, No. 4, 01.04.2017, p. 1016-1020.

Research output: Contribution to journalArticle

Warren, Dan L. ; Geneva, Anthony J. ; Lanfear, Robert ; Rosenberg, Michael. / RWTY (R We There Yet) : An R package for examining convergence of Bayesian phylogenetic analyses. In: Molecular Biology and Evolution. 2017 ; Vol. 34, No. 4. pp. 1016-1020.
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