BEAST 2

BEAST Features

The tables below list the main evolutionary models supported by BEAST 2. For ease of comparison BEAST 1 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" column are to the paper that describes the implementation of the model in the BEAST framework.

Framework

BEAST 2 BEAST 1
Manuscript beast2 beast1.4, beast1.7, beast1.10
Website beast2.org beast.community

Birth-death tree priors

BEAST 2 BEAST 1 Model reference TUTORIAL or XML Package
Birth-death contemporary skyline stadler2013 x stadler2013 BDSKY_contemp.xml bdsky
Birth-death incomplete sampling (no ψ) stadler2009 gernhard2008 stadler2009gernhard2008 - core
Birth-death serial sampling stadler2013 stadler2012 stadler2010stadler2012 BDSKY_sequential.xml bdsky
Birth-death serial skyline stadler2013 x stadler2013 BDSKY_sequential.xml bdsky
Birth-death SIR kühnert2014 x kühnert2014 BDSIR.xml phylodynamics
Calibrated birth-death heled2014 x heled2014 - core
Fossilized birth-death process gavryushkina2014 x gavryushkina2014 bears.xml sampled-ancestors
Yule with one calibration heled2012 heled2012 heled2012 testCalYule_5t_2c.xml core
Yule YuleModel YuleModel yule1924gernhard2008 testYuleOneSite.xml core

Clock models

BEAST 2 BEAST 1 Model reference TUTORIAL or XML Package
Auto-correlated relaxed molecular clock ho2005 thorne1998 - -
Model-averaged uncorrelated relaxed molecular clock issue #170 li2012 li2012 - -
Random local molecular clock drummond2010 drummond2010 drummond2010 testRandomLocalClock.xml core
Strict molecular clock StrictClockModel StrictClockBranchRates zuckerkandl1965 testStrictClock.xml core
Uncorrelated lognormal relaxed molecular clock drummond2006 drummond2006 drummond2006 testRelaxedClock.xml core

Coalescent tree priors

BEAST 2 BEAST 1 Model reference TUTORIAL or XML Package
Bayesian skygrid gill2013 gill2013 gill2013 - beast-classic
Bayesian skyline drummond2005 drummond2005 drummond2005 testBSP.xml core
Constant size drummond2002 drummond2002 kingman1982 testCoalescent.xml core
Deterministic closed SIR popinga2014 dearlove2013 volz2012 DeterCoalSIR_HIVcluster1.xml phylodynamics
Expansion growth griffiths1994 - beast-classic
Exponential growth drummond2002 drummond2002 kuhner1998 testExponentialGrowth.xml core
Extended Bayesian skyline heled2008 heled2008 heled2008 testEBSP.xml core
GMRF Bayesian Skyride minin2008 minin2008 minin2008 testSkyRide.xml beast-classic
Logistic growth - beast-classic
Stochastic closed SIR popinga2014 x popinga2014 StochCoalSIR_HIVcluster1.xml phylodynamics

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 sainudiin2004wu2011 - BEASTvntr
Morphological characters data type StandardDataIntegerData x - core

Miscellaneous

BEAST 2 BEAST 1 Model reference TUTORIAL or XML Package
Bayes factor delimitation of species Leaché2014 x Leaché2014 BFD-tutorial-2017.zip SNAPP
Epoch models x bielejec2013 bielejec2013 - -
Lie Markov models woodhams2014 x woodhams2014 testLieMarkov.xml LMM
Scripting beastshell x NA - beastshell
Sequence error (and post-mortem damage) models Issue 173 rambaut2009 rambaut2009 - -
Spherical diffusion model bouckaert2015 x bouckaert2015 tutorial beast-geo
Tip-date sampling shapiro2011 shapiro2011 drummond2002 (Section 6.3) sampling-tip-dates core

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

BEAST 2 BEAST 1 Model reference TUTORIAL or XML Package
Biased diffusion x - -
Break-away model for phylogeography Bouckaert2017 Bouckaert2017 break-away-phylogeography.html break_away
Models for discrete morphological data Lewis&Olmstead2001 x Lewis&Olmstead2001 examples morph-models
Discrete-state "mugration" model lemey2009 lemey2009 lemey2009 H5N1_HA_discrete2.xml beast-classic
Generalized linear model x in revision - -
Landscape-aware model bouckaert2012 x bouckaert2012 - -
Relaxed random-walk model lemey2010 lemey2010 lemey2010 RacRABV_LogNRRW2.xml beast-classic
Spherical diffusion phylogeography Bouckaert2015 Bouckaert2015 phylogeography_s.0.1.2.pdf GEO_SPHERE
Structured birth-death model kühnert2016 x kühnert2016 Structured-birth-death-model bdmm
Structured coalescent vaughan2014 x vaughan2014 structuredCoalescent.xml MultiTypeTree

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

BEAST 2 BEAST 1 Model reference TUTORIAL or XML Package
Codon position model (SRD06) shapiro2006 shapiro2006 goldman1994 testSRD06.xml core
Covarion model BinaryCovarion BinaryCovarionModel tuffley&steel1996 - core
GTR GTR GTR tavare1986 testGTR.xml core
HKY85 HKY HKY hasegawa1985 testHKY.xml core
Jukes-Cantor (JC69) JukesCantor (use HKY, equal freqs, kappa=1) Jukes & Cantor (1969) testJukesCantor.xml core
Codon substitution model M0 (GY94) xie&bouckaert2018 MG94CodonModel goldman&yang1994yang2000 testM0.xml codonsubstmodels
Microsatellite models sainudiin2004 wu2011 sainudiin2004wu2011 - BEASTvntr
Model averaging & comparison bouckaertDrummond2017 x bouckaertDrummond2017 wiki bModelTest
Gamma-distributed rate heterogeneity among sites SiteModel GammaSiteRateModel yang1994 Introduction-to-BEAST2 core
Reversible-jump Based (RB) RB x bouckaert2013 testApe.xml RBS
SYM SYM x zharkikh1994 testSYM.xml core
TIM TIM x posada2003 testTIM.xml core
TN93 TN93 TN93 tamura1993 testTN93.xml core
TVM TVM x posada2003 testTVM.xml core

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

Bayesian evolutionary analysis by sampling trees

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