BEAST

BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.


References in zbMATH (referenced in 41 articles , 1 standard article )

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  1. Borges, Rui; Kosiol, Carolin: Consistency and identifiability of the polymorphism-aware phylogenetic models (2020)
  2. Everitt, Richard G.; Culliford, Richard; Medina-Aguayo, Felipe; Wilson, Daniel J.: Sequential Monte Carlo with transformations (2020)
  3. Grindstaff, Gillian; Owen, Megan: Representations of partial leaf sets in phylogenetic tree space (2019)
  4. Johndrow, James E.; Palacios, Julia A.: Exact limits of inference in coalescent models (2019)
  5. Keefe, Matthew J.; Ferreira, Marco A. R.; Franck, Christopher T.: Objective Bayesian analysis for Gaussian hierarchical models with intrinsic conditional autoregressive priors (2019)
  6. Warnow, Tandy (ed.): Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret (2019)
  7. Bartoszek, Krzysztof: Exact and approximate limit behaviour of the Yule tree’s cophenetic index (2018)
  8. Kendall, Michelle; Ayabina, Diepreye; Xu, Yuanwei; Stimson, James; Colijn, Caroline: Estimating transmission from genetic and epidemiological data: a metric to compare transmission trees (2018)
  9. Stadler, Tanja; Gavryushkina, Alexandra; Warnock, Rachel C. M.; Drummond, Alexei J.; Heath, Tracy A.: The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes (2018)
  10. Whidden, Chris; Iv, Frederick A. Matsen: Efficiently inferring pairwise subtree prune-and-regraft adjacencies between phylogenetic trees (2018)
  11. Bordewich, Magnus; Linz, Simone; Semple, Charles: Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks (2017)
  12. Jones, Graham: Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent (2017)
  13. Kaehler, Benjamin D.: Full reconstruction of non-stationary strand-symmetric models on rooted phylogenies (2017)
  14. Sumner, Jeremy G.; Jarvis, Peter D.; Francis, Andrew R.: A representation-theoretic approach to the calculation of evolutionary distance in bacteria (2017)
  15. Whidden, Chris; Matsen, Frederick A. IV: Ricci-Ollivier curvature of the rooted phylogenetic subtree-prune-regraft graph (2017)
  16. Gavryushkin, Alex; Drummond, Alexei J.: The space of ultrametric phylogenetic trees (2016)
  17. Guindon, Stéphane; Guo, Hongbin; Welch, David: Demographic inference under the coalescent in a spatial continuum (2016)
  18. Kimmel, Marek; Wojdyła, Tomasz: Genetic demographic networks: mathematical model and applications (2016)
  19. Rey, David; Gardner, Lauren; Waller, S. Travis: Finding outbreak trees in networks with limited information (2016)
  20. Cybis, Gabriela B.; Sinsheimer, Janet S.; Bedford, Trevor; Mather, Alison E.; Lemey, Philippe; Suchard, Marc A.: Assessing phenotypic correlation through the multivariate phylogenetic latent liability model (2015)

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