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 language | English (US) |
|---|---|
| Pages (from-to) | 1016-1020 |
| Number of pages | 5 |
| Journal | Molecular Biology and Evolution |
| Volume | 34 |
| Issue number | 4 |
| DOIs | |
| State | Published - Apr 1 2017 |
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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 journal › Article
}
TY - JOUR
T1 - RWTY (R We There Yet)
T2 - An R package for examining convergence of Bayesian phylogenetic analyses
AU - Warren, Dan L.
AU - Geneva, Anthony J.
AU - Lanfear, Robert
AU - Rosenberg, Michael
PY - 2017/4/1
Y1 - 2017/4/1
N2 - 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.
AB - 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.
KW - Convergence
KW - MCMC
KW - MCMC
KW - Phylogenetics
KW - Stationarity
KW - Topology
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UR - http://www.scopus.com/inward/citedby.url?scp=85018988092&partnerID=8YFLogxK
U2 - 10.1093/molbev/msw279
DO - 10.1093/molbev/msw279
M3 - Article
C2 - 28087773
AN - SCOPUS:85018988092
VL - 34
SP - 1016
EP - 1020
JO - Molecular Biology and Evolution
JF - Molecular Biology and Evolution
SN - 0737-4038
IS - 4
ER -