BEAST Features

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.

General features

BEAST 2.x BEAST 1.8 Model reference Example XML (2.x) Package (2.x)
Framework
Manuscript beast2 beast14, beast17
Website [1] [2]
Data type
DNA/RNA Nucleotide Nucleotides testRNA.xml core
Amino acid Aminoacid AminoAcids core
Binary Binary TwoStates core
Microsatellite Issue #4 wu2011 sainudiin2004, wu2011 x x
Tree models
Bifurcating contemporaneous time-tree
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
Simulation
Sequence alignment simulation seqgen seqgen testSeqGen.xml core
Tree and phylodynamics simulation (MASTER) vaughan2013 x vaughan2013 examples in 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 (in trunk) core
HKY85 HKY HKY hasegawa1985 testHKY.xml core
TN93 TN93 TN93 tamura1993 testTN93.xml core
GTR GTR GTR tavare1986 testGTR.xml core
Gamma-distributed rate heterogeneity among sites yang1994 core
Codon position model (SRD06) shapiro2006 shapiro2006 goldman1994 testSRD06.xml core
Reversible-jump Based (RB) RB x bouckaert2013 testApe.xml RBS
Covarion model [3] [4] core
Microsatellite models Issue #4 wu2011 wu2011

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 x x
Expansion growth x griffiths1994 x x
Bayesian skyline drummond2005 drummond2005 drummond2005 testBSP.xml core
Extended Bayesian skyline heled2008 heled2008 heled2008 testEBSP.xml core
GMRF Bayesian Skyride Issue #172 minin2008 minin2008 x x
Bayesian skygrid Issue #131 gill2013 gill2013 x x
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 yule1924 testYuleOneSite.xml core
Yule with one calibration heled2012 heled2012 heled2012 testCalYule_5t_2c.xml core
Birth-death (with incomplete sampling) stadler2009 gernhard2008 gernhard2008, stadler2009 core
Calibrated birth-death heled2014 x heled2013
Birth-death serial sampling stadler2012 stadler2012 stadler2012 core
Birth-death serial skyline stadler2013 x stadler2013 BDSKY_contemp.xml bdssm
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
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 structuredCoalescent.xml MultiTypeTree
Structured birth-death model in preparation x

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 Issue #41 shapiro2011 drummond2002, Section 6.3 x x
Lie Markov models [5] x [6] LMM
Spherical diffusion model [7] x bouckaert2015 GEO_SPHERE
DISSECT [9] [10] [11] DISSECT
STACEY [12] x [13] STACEY
Scripting beastshell x NA BEASTShell

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Bayesian evolutionary analysis by sampling trees

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