BEAST Comparison

The table below attempts to list the main models supported by BEAST2. For ease of comparison BEAST 1.8 is also included, but you should consult the BEAST1 website for definitive information about that program. Green means the model has been published and extensively tested. Yellow means the method has either not yet been published in a peer-reviewed journal, or that it has been implemented (and perhaps published) but not extensively tested for general use. The “Model reference” is the citation for the first description of the model (not necessarily in a Bayesian context). The links to papers in the “BEAST 2.1” column are to the paper that describes the implementation of the model in the BEAST framework.

Features of BEAST
BEAST 2.1 BEAST 1.8 Model reference Example XML (2.1) Package (2.1)
Manuscript submitted beast14 beast17
Website [1] [2]
Tree models
Bifurcating contemporaneous time-tree
Bifurcating heterochronous time-tree
Sampled-ancestor time-tree in preparation x gavryushkina2013
ClonalOrigin ancestral gene-conversion graph in preparation x didelot2010
Coalescent tree priors
Constant size drummond2002 drummond2002 kingman1982
Exponential growth drummond2002 drummond2002 kuhner1998
Bayesian skyline drummond2005 drummond2005 drummond2005
Extended Bayesian skyline heled2008 heled2008 heled2008
Bayesian skygrid x gill2013 gill2013
Deterministic closed SIR in preparation dearlove2013 volz2012
Birth-death tree priors
Yule yule1924
Yule with one calibration heled2012 heled2012
Birth-death gernhard2008
Calibrated birth-death heled2013 x heled2013
Birth-death with incomplete sampling x stadler2009
Birth-death serial sampling stadler2012 x stadler2012
Birth-death serial skyline stadler2013 x stadler2013
Birth-death SIR kuhnert2013 x kuhnert2013
Statistical phylogeography
Discrete-state “mugration” model lemey2009 lemey2009
“Relaxed random-walk” model lemey2010 lemey2010
“Landscape-aware” model bouckaert2012 x bouckaert2012
Generalized linear model x in revision
Biased diffusion x
Structured coalescent in revision x
Trait evolution
Antigenic evolution x bedford2013 bedford2013
Partition models
Dirichlet process prior site partition model wu2013 x wu2013
Dirichlet process site-block partition model in preparation x
Reversible-jump partition boundary model in preparation x
Species tree / Multispecies coalescent models
*BEAST, multi-{species, gene, individual} heled2010 heled2010 heled2010
SNAPP (for SNP data) bryant2012 x bryant2012
Complete transmission trees x submitted vrancken2013
Sequence alignment simulation
MASTER phylodynamics simulation vaughan2013 x vaughan2013
Epoch models x bielejec2013 bielejec2013

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Bayesian evolutionary analysis by sampling trees