RWTY (R We There Yet): An R Package for Examining Convergence of Bayesian Phylogenetic Analyses

Dan L Warren; Anthony J Geneva; Robert Lanfear

doi:10.1093/molbev/msw279

RWTY (R We There Yet): An R Package for Examining Convergence of Bayesian Phylogenetic Analyses

Mol Biol Evol. 2017 Apr 1;34(4):1016-1020. doi: 10.1093/molbev/msw279.

Authors

Dan L Warren¹, Anthony J Geneva², Robert Lanfear^{1

3}

Affiliations

¹ Department of Biological Sciences, Macquarie University, Sydney, Australia.
² Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA.
³ Division of Evolution, Ecology, and Genetics, Australian National University, Canberra, Australia.

PMID: 28087773
DOI: 10.1093/molbev/msw279

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.

Keywords: MCMC; convergence; phylogenetics; stationarity; topology.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Bayes Theorem
Humans
Markov Chains
Models, Genetic
Monte Carlo Method
Phylogeny
Reproducibility of Results
Sequence Analysis, DNA / methods*
Software