The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics
Open accessAbstract
Summary: A key element to a successful Markov chain Monte Carlo (MCMC) inference is the programming and run performance of the Markov chain. However, the explicit use of quality assessments of the MCMC simulations—convergence diagnostics—in phylogenetics is still uncommon. Here, we present a simple tool that uses the output from MCMC simulations and visualizes a number of properties of primary interest in a Bayesian phylogenetic analysis, such as convergence rates of posterior split probabilities and branch lengths. Graphical exploration of the output from phylogenetic MCMC simulations gives intuitive and often crucial information on the success and reliability of the analysis. The tool presented here complements convergence diagnostics already available in other software packages primarily designed for other applications of MCMC. Importantly, the common practice of using trace-plots of a single parameter or summary statistic, such as the likelihood score of sampled trees, can be misleading for assessing the success of a phylogenetic MCMC simulation. Availability: The program is available as source under the GNU General Public License and as a web application at http://ceb.scs.fsu.edu/awty Contact: jwilgenb@scs.fsu.edu
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Cites
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Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018) · Systematic Biology · doi:10.1093/sysbio/syy032 · Cited by 11,159
Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa
Ariyawansa, H. A., Hyde, K. D., Jayasiri, S. C., Buyck, B., Chethana, K. W. T., Dai, D. Q., Dai, Y. C., Daranagama, D. A., Jayawardena, R. S., Lücking, R., et al. (2015) · Fungal Diversity · doi:10.1007/s13225-015-0346-5 · Cited by 751
Recognition of seven species in the Cryptococcus gattii/Cryptococcus neoformans species complex
Hagen, F., Khayhan, K., Theelen, B., Kolecka, A., Polacheck, I., Sionov, E., Falk, R., Parnmen, S., Lumbsch, H. T., & Boekhout, T. (2015) · Fungal Genetics and Biology · doi:10.1016/j.fgb.2015.02.009 · Cited by 687
Bayesian Evolutionary Analysis with BEAST
Drummond, A. J., & Bouckaert, R. R. (2015) · Cambridge University Press eBooks · doi:10.1017/cbo9781139095112 · Cited by 527
Ribas, C. C., Aleixo, A., Nogueira, A. C. R., Miyaki, C. Y., & Cracraft, J. (2012) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2011.1120 · Cited by 517
Metadata
- Authors
- Nylander, J. A. A., Wilgenbusch, J. C., Warren, D. L., & Swofford, D. L.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-08-30
- Volume
- 24
- Issue
- 4
- Pages
- 581-583
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2128841626
- Cited by
- 1,747
- References
- 10
- FWCI
- 97.60
- Type
- journal article
- Language
- en
- Open access
- hybrid
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