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 13 articles , 1 standard article )

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  1. Jones, Graham: Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent (2017)
  2. Gavryushkin, Alex; Drummond, Alexei J.: The space of ultrametric phylogenetic trees (2016)
  3. Drummond, Alexei J.; Bouckaert, Remco R.: Bayesian evolutionary analysis with BEAST (2015)
  4. Höhna, Sebastian: The time-dependent reconstructed evolutionary process with a key-role for mass-extinction events (2015)
  5. RoyChoudhury, Arindam; Willis, Amy; Bunge, John: Consistency of a phylogenetic tree maximum likelihood estimator (2015)
  6. Spade, David A.; Herbei, Radu; Kubatko, Laura S.: Geometric ergodicity of a hybrid sampler for Bayesian inference of phylogenetic branch lengths (2015)
  7. Lopez, M.Graham; Horton, Mitchel D.: Batch matrix exponentiation (2014)
  8. Fajardo, David; Gardner, Lauren M.: Inferring contagion patterns in social contact networks with limited infection data (2013)
  9. Leviyang, Sivan: The coalescence of intrahost HIV lineages under symmetric CTL attack (2012)
  10. Leviyang, Sivan: Sampling HIV intrahost genealogies based on a model of acute stage CTL response (2012)
  11. Pratas, Frederico; Trancoso, Pedro; Sousa, Leonel; Stamatakis, Alexandros; Shi, Guochun; Kindratenko, Volodymyr: Fine-grain parallelism using multi-core, cell/BE, and GPU systems (2012) ioport
  12. Jones, Graham: Calculations for multi-type age-dependent binary branching processes (2011)
  13. Maruvka, Yosef E.; Shnerb, Nadav M.; Solomon, Sorin; Yaari, Gur; Kessler, David A.: Slicing and dicing the genome: A statistical physics approach to population genetics (2011)