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.

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

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