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 23 articles , 1 standard article )

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  1. Bordewich, Magnus; Linz, Simone; Semple, Charles: Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks (2017)
  2. Jones, Graham: Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent (2017)
  3. Kaehler, Benjamin D.: Full reconstruction of non-stationary strand-symmetric models on rooted phylogenies (2017)
  4. Whidden, Chris; Matsen, Frederick A.IV: Ricci-Ollivier curvature of the rooted phylogenetic subtree-prune-regraft graph (2017)
  5. Gavryushkin, Alex; Drummond, Alexei J.: The space of ultrametric phylogenetic trees (2016)
  6. Guindon, Stéphane; Guo, Hongbin; Welch, David: Demographic inference under the coalescent in a spatial continuum (2016)
  7. Kimmel, Marek; Wojdyła, Tomasz: Genetic demographic networks: mathematical model and applications (2016)
  8. Rey, David; Gardner, Lauren; Waller, S.Travis: Finding outbreak trees in networks with limited information (2016)
  9. 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)
  10. Drummond, Alexei J.; Bouckaert, Remco R.: Bayesian evolutionary analysis with BEAST (2015)
  11. Höhna, Sebastian: The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events (2015)
  12. RoyChoudhury, Arindam; Willis, Amy; Bunge, John: Consistency of a phylogenetic tree maximum likelihood estimator (2015)
  13. Spade, David A.; Herbei, Radu; Kubatko, Laura S.: Geometric ergodicity of a hybrid sampler for Bayesian inference of phylogenetic branch lengths (2015)
  14. Lopez, M.Graham; Horton, Mitchel D.: Batch matrix exponentiation (2014)
  15. Weiss, Robert E.; Suchard, Marc A.: Comment on article by Rubio and Steel (2014)
  16. Fajardo, David; Gardner, Lauren M.: Inferring contagion patterns in social contact networks with limited infection data (2013)
  17. Palacios, Julia A.; Minin, Vladimir N.: Gaussian process-based Bayesian nonparametric inference of population size trajectories from gene genealogies (2013)
  18. Gong, Yu-Nong; Chen, Guang-Wu; Suchard, Marc A.: A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses (2012)
  19. Leviyang, Sivan: The coalescence of intrahost HIV lineages under symmetric CTL attack (2012)
  20. Leviyang, Sivan: Sampling HIV intrahost genealogies based on a model of acute stage CTL response (2012)

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