The tables below list the main evolutionary models supported by BEAST 2. For ease of comparison BEAST 1.8 is also included. 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 original description of the model (not necessarily in a Bayesian context). The links to papers in the "BEAST 2.x" column are to the paper that describes the implementation of the model in the BEAST framework.
Keeping this table up-to-date is rather challenging, and BEAST 2 has seen rapid development, for definitive information on BEAST 1.8 you should consult the BEAST1 website, and for BEAST 2, the package overview on CBAN.
Framework
| BEAST 2 | BEAST 1 | |
|---|---|---|
| Manuscript | beast2 | beast1.4, beast1.7, beast1.10 |
| Website | beast2.org | beast.community |
Birth-death tree priors
Clock models
Coalescent tree priors
Data type
| BEAST 2 | BEAST 1 | Model reference | TUTORIAL or XML | Package | |
|---|---|---|---|---|---|
| Amino acid data type | Aminoacid | AminoAcids | - | core | |
| Binary data type | Binary | TwoStates | - | core | |
| DNA and RNA data type | Nucleotide | Nucleotides | testRNA.xml | core | |
| Microsatellite data type | sainudiin2004 | wu2011 | sainudiin2004 , wu2011 | - | BEASTvntr |
| Morphological characters data type | StandardData , IntegerData | x | - | core |
Miscellaneous
Partition models
| BEAST 2 | BEAST 1 | Model reference | TUTORIAL or XML | Package | |
|---|---|---|---|---|---|
| Dirichlet process prior site partition model | wu2013 | x | wu2013 | mammal_sdpm2_sc.xml | substBMA |
Phylogeography
Simulation
| BEAST 2 | BEAST 1 | Model reference | TUTORIAL or XML | Package | |
|---|---|---|---|---|---|
| Sequence alignment simulation | seqgen | seqgen | testSeqGen.xml | core | |
| Tree and phylodynamics simulation (MASTER) | vaughan2013 | x | wiki#tutorials | MASTER |
Species or Hierarchical tree priors
| BEAST 2 | BEAST 1 | Model reference | TUTORIAL or XML | Package | |
|---|---|---|---|---|---|
| Complete transmission trees | x | vrancken2014 | vrancken2014 | - | - |
| SNAPP (for SNP data) | bryant2012 | x | bryant2012 | test1.xml | SNAPP |
| Species delimitation under multispecies | STACEY | DISSECT | jones2017 | - | STACEY |
| StarBEAST, multi-{species, gene, individual} | heled2010 | heled2010 | heled2010 | testStarBeast.xml | core |
| StarBEAST2 | ogilvie2016 | x | ogilvie2016 | tutorial | starbeast2 |
Substitution models
Trait evolution
| BEAST 2 | BEAST 1 | Model reference | TUTORIAL or XML | Package | |
|---|---|---|---|---|---|
| Antigenic evolution | x | bedford2013 | bedford2013 | - | - |
Tree models
| BEAST 2 | BEAST 1 | Model reference | TUTORIAL or XML | Package | |
|---|---|---|---|---|---|
| Bifurcating contemporaneous time-tree | - | core | |||
| Bifurcating heterochronous time-tree | testTipDates.xml | core | |||
| ClonalOrigin ancestral gene-conversion graph | vaughan2017 | x | didelot2010 | basic_tutorial.html | bacter |
| Sampled ancestor time-tree | gavryushkina2014 | x | gavryushkina2014 | testSA.xml | sampled-ancestors |