Results 1 to 10 of about 35,412 (173)
Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 [PDF]
Systematic Biology, 2018 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.
Andrew Rambaut +2 more
exaly +9 more sources
Scalable Bayesian phylogenetics. [PDF]
Philos Trans R Soc Lond B Biol Sci, 2022 Recent advances in Bayesian phylogenetics offer substantial computational savings to accommodate increased genomic sampling that challenges traditional inference methods. In this review, we begin with a brief summary of the Bayesian phylogenetic framework, and then conceptualize a variety of methods to improve posterior approximations via Markov chain ...
Fisher AA +5 more
europepmc +5 more sources
Data integration in Bayesian phylogenetics. [PDF]
Annu Rev Stat Appl, 2023 Researchers studying the evolution of viral pathogens and other organisms increasingly encounter and use large and complex data sets from multiple different sources. Statistical research in Bayesian phylogenetics has risen to this challenge. Researchers use phylogenetics not only to reconstruct the evolutionary history of a group of organisms, but ...
Hassler GW +7 more
europepmc +5 more sources
Variational Supertrees for Bayesian Phylogenetics. [PDF]
Bull Math BiolAbstractBayesian phylogenetic inference is powerful but computationally intensive. Researchers may find themselves with two phylogenetic posteriors on overlapping data sets and may wish to approximate a combined result without having to re-run potentially expensive Markov chains on the combined data set.
Karcher MD, Zhang C, Matsen FA.
europepmc +4 more sources
Hamiltonian Monte Carlo sampling to estimate past population dynamics using the skygrid coalescent model in a Bayesian phylogenetics framework [version 1; peer review: 1 approved, 2 approved with reservations] [PDF]
Wellcome Open Research, 2020 Nonparametric coalescent-based models are often employed to infer past population dynamics over time. Several of these models, such as the skyride and skygrid models, are equipped with a block-updating Markov chain Monte Carlo sampling scheme to ...
Guy Baele +3 more
doaj +2 more sources
Metagenomic sequencing, molecular characterization, and Bayesian phylogenetics of imported type 2 vaccine-derived poliovirus, Spain, 2021 [PDF]
Frontiers in Cellular and Infection Microbiology, 2023 IntroductionIn 2021, a type 2 vaccine-derived poliovirus (VDPV2) was isolated from the stool of a patient with acute flaccid paralysis (AFP) admitted to Spain from Senegal. A virological investigation was conducted to characterize and trace the origin of
Maria Dolores Fernandez-Garcia +12 more
doaj +2 more sources
Fidelity of hyperbolic space for Bayesian phylogenetic inference.
PLoS Computational Biology, 2023 Bayesian inference for phylogenetics is a gold standard for computing distributions of phylogenies. However, Bayesian phylogenetics faces the challenging computational problem of moving throughout the high-dimensional space of trees.
Matthew Macaulay +2 more
doaj +4 more sources
Long-branch attraction bias and inconsistency in Bayesian phylogenetics. [PDF]
PLoS ONE, 2009 Bayesian inference (BI) of phylogenetic relationships uses the same probabilistic models of evolution as its precursor maximum likelihood (ML), so BI has generally been assumed to share ML's desirable statistical properties, such as largely unbiased ...
Bryan Kolaczkowski, Joseph W Thornton
doaj +2 more sources
MRBAYES: Bayesian inference of phylogenetic trees [PDF]
Bioinformatics, 2001 Abstract Summary: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. Availability: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
John P Huelsenbeck, Fredrik Ronquist
exaly +3 more sources
Recent advances in the inference of deep viral evolutionary history [PDF]
Journal of VirologyThe rapid rate of virus evolution, while useful for outbreak investigations, poses a challenge for accurately estimating long-term viral evolutionary divergence and leaves us with little genomic traces at deep evolutionary timescales, complicating the ...
Jonathon C. O. Mifsud +3 more
doaj +2 more sources