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

Date

2017

Authors

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

Journal Title

Journal ISSN

Volume Title

Publisher

Society for Molecular Biology Evolution

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.

Description

Keywords

MCMC, phylogenetics, topology, MCMC, convergence, stationarity

Citation

Source

Molecular Biology and Evolution

Type

Journal article

Book Title

Entity type

Access Statement

Open Access

License Rights

DOI

10.1093/molbev/msw279

Restricted until