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

Dan L. Warren | Zendy; Anthony J. Geneva | Zendy; Robert Lanfear | Zendy

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

Author(s) -

Dan L. Warren,

Anthony J. Geneva,

Robert Lanfear

Publication year - 2016

Publication title -

molecular biology and evolution

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 6.637

H-Index - 218

eISSN - 1537-1719

pISSN - 0737-4038

DOI - 10.1093/molbev/msw279

Subject(s) - markov chain monte carlo , phylogenetic tree , bayesian probability , convergence (economics) , biology , bayesian inference , inference , markov chain , reliability (semiconductor) , posterior probability , r package , tree (set theory) , component (thermodynamics) , computer science , data mining , evolutionary biology , machine learning , statistics , artificial intelligence , mathematics , genetics , combinatorics , power (physics) , physics , quantum mechanics , economics , gene , economic growth , thermodynamics

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.

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