Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7
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Summary
The software package Tracer is presented, for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference, which provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more.
- Type
- article
- Published
- 2018-04-27
- Cited by
- 9,632
- References
- 21
- Access
- Open access
- OpenAlex
- https://openalex.org/W2801159594
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:21388879
Keywords
Markov chain Monte Carlo, Posterior probability, Bayesian probability, Bayesian inference, Computer science
References
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- Host Phylogeny Constrains Cross-Species Emergence and Establishment of Rabies Virus in Bats
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- LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters
- Bayesian Phylogenetics with BEAUti and the BEAST 1.7
- Inference from Iterative Simulation Using Multiple Sequences
- MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
- Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
- Bayesian coalescent inference of past population dynamics from molecular sequences.
- Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics.
- Comparison of Bayesian and maximum-likelihood inference of population genetic parameters
- Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints
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- Evolutionary Sample Size and Consilience in Phylogenetic Comparative Analysis.
- Uncertainty in Phylogenetic Tree Estimates
- 150 million years of sustained increase in pterosaur flight efficiency
- Genetic structure of the grey side-gilled sea slug (Pleurobranchaea maculata) in coastal waters of New Zealand
- Genomic Epidemiology Reconstructs the Introduction and Spread of Zika Virus in Central America and Mexico
- Chronic and Occult Hepatitis B Virus Infection in Pregnant Women in Botswana
- Revisiting the phylogeny of Ficus (Moraceae): When Next Generation Sequencing corroborates Past Generation Botanists
- The effect of dictionary omissions on phylogenies computationally inferred from lexical data
- Next-generation museum genomics: Phylogenetic relationships among palpimanoid spiders using sequence capture techniques (Araneae: Palpimanoidea).
- Evidence for Miocene overwater colonization in Caribbean Cyrtognatha spiders
- Exploring the generic delimitation of Phyllagathis and Bredia (Melastomataceae): A combined nuclear and chloroplast DNA analysis
- Integrative description of Macrobiotus canaricus sp. nov. with notes on M. recens (Eutardigrada: Macrobiotidae)
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- Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages
- The unusual flagellar-targeting mechanism and functions of the trypanosome ortholog of the ciliary GTPase Arl13b
- Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origins
- Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion
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