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.
| BEAST 2.1 | BEAST 1.8 | Model reference | Example XML (2.1) | Package (2.1) | |
|---|---|---|---|---|---|
| Framework | |||||
| 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 | ||
| Simulation | |||||
| Sequence alignment simulation | |||||
| MASTER phylodynamics simulation | vaughan2013 | x | vaughan2013 | ||
| Miscellaneous | |||||
| Epoch models | x | bielejec2013 | bielejec2013 | ||