The DOI matches its Crossref record; 22 of the 22 references it cites were found in a registry or an index.
Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7
Open accessAbstract
Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular sequence data. Visualizing and analyzing the MCMC-generated samples from the posterior distribution is a key step in any non-trivial Bayesian inference. We present the software package Tracer (version 1.7) for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more. Tracer is open-source and available at http://beast.community/tracer.
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“We checked for convergence between runs using Tracer v. 1.7 [36], ensuring that ESS values were >200 to indicate adequate sampling.”
From Mitogenomic Crocodylia phylogeny and population structure of Crocodylus porosus including the extinct Seychelles crocodile (2026) · cites this paper as [36]
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“We ran eight independent MCMC chains and assessed convergence from effective sample sizes in Tracer (78)”
From Convergent genome streamlining accompanies independent miniaturization in the world’s smallest fishes (2026) · cites this paper as [78]
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MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A. E., Höhna, S., Larget, B. R., Liu, L., Suchard, M. A., & Huelsenbeck, J. P. (2012) · Systematic Biology · doi:10.1093/sysbio/sys029 · Cited by 28,399 · cited 2×
“2014), LAMARC (Kuhner 2006), Migrate (Beerli 2006), MrBayes (Ronquist et al. 2012), RevBayes (Höhna et al.”
MethodSelf-citationInference from iterative simulation using multiple sequences
Gelman, A., & Rubin, D. B. (1992) · Statistical Science · doi:10.1214/ss/1177011136 · Cited by 16,627 · cited 1×
“, Gelman–Rubin diagnostics (Gelman and Rubin 1992) that Tracer currently does not provide.”
BackgroundBayesian Phylogenetics with BEAUti and the BEAST 1.7
Drummond, A. J., Suchard, M. A., Xie, D., & Rambaut, A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss075 · Cited by 10,128 · cited 3×
“Tracer works automatically with sample output from BEAST (Drummond et al. 2012), BEAST2 (Bouckaert et al.”
MethodSelf-citationBEAST 2: a software platform for Bayesian evolutionary analysis
Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C.-H., Xie, D., Suchard, M. A., Rambaut, A., & Drummond, A. J. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003537 · Cited by 6,527 · cited 2×
“2012), BEAST2 (Bouckaert et al. 2014), LAMARC (Kuhner 2006), Migrate (Beerli 2006), MrBayes (Ronquist et al.”
MethodSelf-citationCODA: convergence diagnosis and output analysis for MCMC
Plummer, M., Best, N., Cowles, K., & Vines, K. (2006) · Open Research Online (The Open University) · Cited by 3,317
Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences
Drummond, A. J. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi103 · Cited by 3,094 · cited 1×
“2002), and the non-parametric Bayesian skyline (Drummond et al. 2005; Heled and Drummond 2008), skyride (Minin et al.”
BackgroundSelf-citationBayesian Phylogeography Finds Its Roots
Lemey, P., Rambaut, A., Drummond, A. J., & Suchard, M. A. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000520 · Cited by 1,784 · cited 1×
“Discrete phylogeographic analyses frequently employ BSSVS due to the potentially large amount of transition rates that need to be estimated (Lemey et al. 2009), but”
Self-citationProbability Distribution of Molecular Evolutionary Trees: A New Method of Phylogenetic Inference
Rannala, B. H., & Yang, Z. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02338839 · Cited by 1,751 · cited 2×
“Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) (Rannala and Yang 1996; Mau et al. 1999; Drummond et al. 2002) flourishes as a popular approach to uncover the evolutionary relationships among taxa, such as genes, genomes, individuals, or species.”
MethodNylander, J. A. A., Wilgenbusch, J. C., Warren, D. L., & Swofford, D. L. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm388 · Cited by 1,751
Drummond, A. J., Nicholls, G. K., Rodrigo, A. G., & Solomon, W. (2002) · Genetics · doi:10.1093/genetics/161.3.1307 · Cited by 1,059
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Self-citationTegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2020) · doi:10.1101/2020.12.21.20248640 · Cited by 2,535
“Convergence of MCMC chains was checked using Tracer v.1.7.1 22 .”
Influential
Metadata
- Authors
- Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A.
- Affiliations
- University of Edinburgh (GB)
- University of Auckland (NZ)
- KU Leuven (BE)
- University of California, Los Angeles (US)
- Corresponding author
- Rambaut, Andrew
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-04-27
- Volume
- 67
- Issue
- 5
- Pages
- 901-904
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- PMC
- PMC6101584
- OpenAlex
- W2801159594
- Cited by
- 11,159
- References
- 22
- Citations by year
- 2026: 1393 · 2025: 1633 · 2024: 1602 · 2023: 1501 · 2022: 1638 · 2021: 1477 · 2020: 1236 · 2019: 574 · 2018: 95
- FWCI
- 301.42
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Systematic Biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Lirias (KU Leuven) (submittedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- Funders
- National Science Foundation (1264153)
- National Institutes of Health (R01 AI107034, U19 AI135995)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Mathematics › Statistics and Probability › Markov Chains and Monte Carlo Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- tracers, Bayesian phylogenetics, kernel density estimation, multivariate data visualization, open source software
- MeSH terms
- Bayes Theorem, Markov Chains, Models, Genetic, Monte Carlo Method, Phylogeny, Software, Evolution, Molecular
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