The tables below list the main evolutionary models supported by BEAST 2. For ease of comparison BEAST 1.8 is also included, but you should consult the BEAST1 website for definitive information about that version of the platform, as keeping this table up-to-date is rather challenging. 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.
Contents
Framework
| BEAST 2.x | BEAST 1.8 | |
|---|---|---|
| Manuscript | beast2 | beast14, beast17 |
| Website | beast2.org | beast.bio.ed.ac.uk |
General features
| BEAST 2.x | BEAST 1.8 | Model reference | TUTORIAL or XML (2.x) | Package (2.x) | |
|---|---|---|---|---|---|
| Data type | |||||
| DNA/RNA | Nucleotide | Nucleotides | testRNA.xml | core | |
| Amino acid | Aminoacid | AminoAcids | x | core | |
| Binary | Binary | TwoStates | x | core | |
| Microsatellite | sainudiin2004 | wu2011 | sainudiin2004, wu2011 | x | BEASTvntr |
| Discrete values (e.g. morphological characters) | StandardData or IntegerData | x | core | ||
| Tree models | |||||
| Bifurcating contemporaneous time-tree | core | ||||
| Bifurcating heterochronous time-tree | testTipDates.xml | core | |||
| Sampled-ancestor time-tree | gavryushkina2014 | x | gavryushkina2014 | testSA.xml | sampled-ancestors |
| ClonalOrigin ancestral gene-conversion graph | vaughan2016 | x | didelot2010 | tutorial | bacter |
| Simulation | |||||
| Sequence alignment simulation | seqgen | seqgen | testSeqGen.xml | core | |
| Tree and phylodynamics simulation (MASTER) | vaughan2013 | x | vaughan2013 | tutorials | MASTER |
Substitution models
| BEAST 2.x | BEAST 1.8 | Model reference | Example XML (2.x) | Package (2.x) | |
|---|---|---|---|---|---|
| Jukes-Cantor (JC69) | JukesCantor | (use HKY, equal freqs, kappa=1) | Jukes & Cantor (1969) | testJukesCantor.xml | core |
| HKY85 | HKY | HKY | hasegawa1985 | testHKY.xml | core |
| TN93 | TN93 | TN93 | tamura1993 | testTN93.xml | core |
| TIM | TIM | x | posada2003 | testTIM.xml | core |
| TVM | TVM | x | posada2003 | testTVM.xml | core | SYM | SYM | x | zharkikh1994 | testSYM.xml | core |
| GTR | GTR | GTR | tavare1986 | testGTR.xml | core |
| Gamma-distributed rate heterogeneity among sites | SiteModel | GammaSiteRateModel | yang1994 | tutorial | core |
| Codon position model (SRD06) | shapiro2006 | shapiro2006 | goldman1994 | testSRD06.xml | core |
| Reversible-jump Based (RB) | RB | x | bouckaert2013 | testApe.xml | RBS |
| Covarion model | BinaryCovarion | BinaryCovarionModel | tuffley&steel1996 | x | core |
| Microsatellite models | sainudiin2004 | wu2011 | sainudiin2004, wu2011 | x | BEASTvntr |
| Model averaging & comparison | bouckaert2016 | ? | bouckaert2016 | tutorial | bModelTest |
Trait evolution
| BEAST 2.x | BEAST 1.8 | Model reference | Example XML (2.x) | Package (2.x) | |
|---|---|---|---|---|---|
| Antigenic evolution | x | bedford2013 | bedford2013 |
Partition models
| BEAST 2.x | BEAST 1.8 | Model reference | Example XML (2.x) | Package (2.x) | |
|---|---|---|---|---|---|
| Dirichlet process prior site partition model | wu2013 | x | wu2013 | primate_SDPM2_sc.xml | subst-bma |
| Dirichlet process site-block partition model | in preparation | x | |||
| Reversible-jump partition boundary model | in preparation | x |
Molecular clock models
| BEAST 2.x | BEAST 1.8 | Model reference | Example XML (2.x) | Package (2.x) | |
|---|---|---|---|---|---|
| Strict molecular clock | StrictClockModel | StrictClockBranchRates | zuckerkandl1965 | testStrictClock.xml | core |
| Uncorrelated lognormal relaxed molecular clock | drummond2006 | drummond2006 | drummond2006 | testRelaxedClock.xml | core |
| Random local molecular clock | drummond2010 | drummond2010 | drummond2010 | testRandomLocalClock.xml | core |
| Model-averaged uncorrelated relaxed molecular clock | issue #170 | li2012 | li2012 | x | x |
| Auto-correlated relaxed molecular clock | x | ho2005 | thorne1998 | x | x |
Coalescent tree priors
| BEAST 2.x | BEAST 1.8 | Model reference | Example XML (2.x) | Package (2.x) | |
|---|---|---|---|---|---|
| Constant size | drummond2002 | drummond2002 | kingman1982 | testCoalescent.xml | core |
| Exponential growth | drummond2002 | drummond2002 | kuhner1998 | testExponentialGrowth.xml | core |
| Logistic growth | x | beast-classic | |||
| Expansion growth | griffiths1994 | x | beast-classic | ||
| Bayesian skyline | drummond2005 | drummond2005 | drummond2005 | testBSP.xml | core |
| Extended Bayesian skyline | heled2008 | heled2008 | heled2008 | testEBSP.xml | core |
| GMRF Bayesian Skyride | minin2008 | minin2008 | minin2008 | testSkyRide.xml | beast-classic |
| Bayesian skygrid | gill2013 | gill2013 | gill2013 | x | beast-classic |
| Deterministic closed SIR | popinga2014 | dearlove2013 | volz2012 | DeterCoalSIR_HIVcluster1.xml | phylodynamics |
| Stochastic closed SIR | popinga2014 | x | popinga2014 | StochCoalSIR_HIVcluster1.xml | phylodynamics |
Birth-death tree priors
| BEAST 2.x | BEAST 1.8 | Model reference | Example XML (2.x) | Package (2.x) | |
|---|---|---|---|---|---|
| Yule | gernhard2008 | yule1924 | testYuleOneSite.xml | core | |
| Yule with one calibration | heled2012 | heled2012 | heled2012 | testCalYule_5t_2c.xml | core |
| Calibrated birth-death | heled2014 | x | heled2014 | x | core |
| Birth-death incomplete sampling (no ψ) | stadler2009 | gernhard2008 | gernhard2008, stadler2009 | x | bdsky |
| Birth-death serial sampling (no time interval) | stadler2010, stadler2012 | stadler2010, stadler2012 | stadler2010, stadler2012 | x | bdsky |
| Birth-death serial skyline | stadler2013 | x | stadler2013 | BDSKY_contemp.xml | bdsky |
| Fossilized birth-death process | gavryushkina2014 | x | heath2014 | bears.xml | sampled-ancestors |
| Birth-death SIR | kühnert2014 | x | kühnert2014 | BDSIR.xml | phylodynamics |
Species tree prior / Hierarchical tree priors
| BEAST 2.x | BEAST 1.8 | Model reference | Example XML (2.x) | Package (2.x) | |
|---|---|---|---|---|---|
| *BEAST, multi-{species, gene, individual} | heled2010 | heled2010 | heled2010 | testStarBeast.xml | core |
| *BEAST2 | ogilvie2016 | x | ogilvie2016 | tutorial | starbeast2 |
| SNAPP (for SNP data) | bryant2012 | x | bryant2012 | test1.xml | SNAPP |
| Complete transmission trees | x | vrancken2014 | vrancken2014 | x | x |
Statistical phylogeography
| BEAST 2.x | BEAST 1.8 | Model reference | Example XML (2.x) | Package (2.x) | |
|---|---|---|---|---|---|
| Discrete-state “mugration” model | lemey2009 | lemey2009 | lemey2009 | H5N1_HA_discrete2 | beast-classic |
| “Relaxed random-walk” model | lemey2010 | lemey2010 | lemey2010 | RacRABV | beast-classic |
| “Landscape-aware” model | bouckaert2012 | x | bouckaert2012 | ||
| Generalized linear model | x | in revision | x | x | |
| Biased diffusion | x | x | x | ||
| Structured coalescent | vaughan2014 | x | vaughan2014 | structuredCoalescent.xml | MultiTypeTree |
| Structured birth-death model | kühnert2016 | x | kühnert2016 | tutorial | bdmm |
| Models for discrete morphological data | Lewis&Olmstead2001 | x | Lewis&Olmstead2001 | XMLs | morph-models |
Miscellaneous
| BEAST 2.x | BEAST 1.8 | Model reference | Example XML (2.x) | Package (2.x) | |
|---|---|---|---|---|---|
| Epoch models | x | bielejec2013 | bielejec2013 | x | x |
| Sequence error (and post-mortem damage) models | Issue #173 | rambaut2009 | rambaut2009 | x | x |
| Tip-date sampling | shapiro2011 | shapiro2011 | drummond2002, Section 6.3 | tutorial | core |
| Lie Markov models | woodhams2014 | x | woodhams2014 | testLieMarkov.xml | LMM |
| Spherical diffusion model | bouckaert2015 | x | bouckaert2015 | beast-geo | beast-geo |
| Species delimitation under multispecies | STACEY | DISSECT | jones2016 | STACEY | |
| Bayes factor delimitation of species | Leaché2014 | x | Leaché2014 | BFD | SNAPP |
| Scripting | beastshell | x | NA | beastshell |