Welcome to Help Me Choose

Standard template

Standard template – clock model panel
Standard template – initialization panel
Standard template – MCMC panel
Standard template – operators panel
Standard template – partitions panel
Standard template – priors panel
Standard template – site model panel
Standard template – starting tree panel
Standard template – tip dates panel

StarBeast3 template

StarBeast3 template – gene clock model panel
StarBeast3 template – gene ploidy panel
StarBeast3 template – species clock model panel
StarBeast3 template – taxon sets panel

Priors

BICEPS tree prior
Birth rate prior
Birth rate rate prior
Calibrated Yule birth rate prior
Clock prior
collapse weight rate prior
Death rate prior
Exponential pop size prior
Frequencies prior
Gamma shape prior
Growth rate prior
Indicators prior
Kappa 1 prior
Kappa 2 prior
Kappa prior
MRCA prior
Mutation rate prior
Pop mean prior
Pop size prior
Population mean prior
Proportion invariable prior
GTR rate priors
Root age prior
Yule birth rate prior
Yule skyline tree prior
Yule-skyline collapse tree prior
See here for tree priors.

Parametric Distributions

Beta alpha
Beta beta
Beta offset
Dirichlet alpha
Dirichlet offset
Exponential mean
Exponential offset
Gamma alpha
Gamma beta
Gamma mode
Gamma offset
Inverse Gamma alpha
Inverse Gamma beta
Inverse Gamma offset
Laplace Distribution mu
Laplace Distribution offset
Laplace Distribution scale
Log Normal Distribution Model M
Log Normal Distribution Model mean In Real Space
Log Normal Distribution Model offset
Log Normal Distribution Model S
Normal mean
Normal offset
Normal sigma
One On X offset
Poisson lambda
Poisson offset
Uniform lower
Uniform offset
Uniform upper

Operators

Bactrian delta exchange operator
Kernel distribution
Bactrian node operator
Bactrian random walk operator
Bactrian rate scale operator
Subtree slide operator
Bactrian tree scale operator
Bactrian up down operator
Bit flip operator
Epoch flex operator
Exchange operator
Operator weight tuning
SampleOffValues operator
Subtree slide operator
Tree stretch operator
Wilson Balding operator

Other

Bayesian skyline
Birth death
Birth rate – dimension
Birth rate – estimate
Birth rate – keys
Birth rate – lower
Birth rate – minordimension
Birth rate – upper
Calibrated Yule model
Cluster tree – adjust tree node heights
Cluster tree – clock.rate
Cluster tree – cluster type
Coalescent constant
Coalescent exponential
Constant population0 pop size
EBSP logger – file name
EBSP logger – log every
EBSP logger – mode
EBSP logger – sanitise headers
EBSP logger – sort
Extended Bayesian skyline
GTR frequencies
GTR rate AC
GTR rate AG
GTR rate AT
GTR rate CG
GTR rate CT
GTR rate GT
HKY frequencies
HKY kappa
Markov chained pop sizes – initial mean
Markov chained pop sizes – jeffreys
Markov chained pop sizes – parameter
Markov chained pop sizes – reverse
Markov chained pop sizes – shape
Markov chained pop sizes – uselog
Markov chained pop sizes – use Log Normal
MCMC chain length
MCMC num initialization attempts
MCMC operator schedule
MCMC pre burnin
MCMC sample from prior
MCMC store every
Newick tree – adjust tip heights
Newick tree – adjust tree node heights
Newick tree – binarize multifurcations
Newick tree – is labelled Newick
Newick tree – newick
Newick tree – offset
Newick tree – scale
Newick tree - singlechild
Newick tree – threshold
Operator schedule – auto optimize
Operator schedule – auto optimize delay
Operator schedule – detailed rejection
Operator schedule — transform
Operator schedule – weight
Operator schedule – weight is percentage
Random local clock – include root
Random local clock – rates are multipliers
Random local clock – rate prior
Random local clock – rate change prior
Random local clock – scaling
Random tree – adjust tree node heights
Random tree – root height
Relaxed clock – normalize
Relaxed Clock – number of discrete rates
Screen log – file name
Screen log – log every
Screen log – mode
Screen log – sanitise headers
Screen log – sort
Site Model gamma category count
Site Model mutation rate
Site Model proportion invariable
Site Model shape
Site model subst model
Species tree logger – file name
Species tree logger – log every
Species tree logger – mode
Species tree logger – sanitise headers
Species tree logger – sort
clock.rate
TN93 frequencies
tn93 kappa1
tn93 kappa2
Trace log – file name
Trace log – log every
Trace log – mode
Trace log – sanitise headers
Trace log – sort
Tree likelihood branch rate model
Tree likelihood site model
Tree log – file name
Tree log – log every
Tree log – mode
Tree log – sanitise headers
Tree log – sort
Yule model

References

Banner KM, Irvine KM, Rodhouse TJ. The use of Bayesian priors in Ecology: The good, the bad and the not great. Methods in Ecology and Evolution. 2020 Aug;11(8):882-9. doi:10.1111/2041-210X.13407.

Bouckaert RR. An Efficient Coalescent Epoch Model for Bayesian Phylogenetic Inference, Systematic Biology, syac015, 2022 doi:10.1093/sysbio/syac015.

Bouckaert RR. OBAMA: OBAMA for Bayesian amino-acid model averaging. PeerJ. 2020 Aug 4;8:e9460. doi:10.7717/peerj.9460.

Bouckaert RR, Drummond AJ. bModelTest: Bayesian phylogenetic site model averaging and model comparison. BMC evolutionary biology. 2017 Dec;17(1):1-1. doi:10.1186/s12862-017-0890-6.

Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS computational biology. 2014 Apr 10;10(4):e1003537. doi:10.1371/journal.pcbi.1003537

Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS computational biology. 2019 Apr 8;15(4):e1006650. doi:10.1371/journal.pcbi.1006650

Douglas J, Jiménez-Silva CL, Bouckaert R. StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent. Systematic Biology. 2022 Feb 17. doi:10.1093/sysbio/syac010.

Douglas J, Zhang R, Bouckaert R. Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model. PLoS computational biology. 2021 Feb 2;17(2):e1008322. doi:10.1371/journal.pcbi.1008322.

Drummond AJ, Ho SY, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS biology. 2006 May;4(5):e88. doi:10.1371/journal.pbio.0040088

Drummond AJ, Rambaut A, Shapiro BE, Pybus OG. Bayesian coalescent inference of past population dynamics from molecular sequences, Molecular Biology and Evolution. 22(5):1185-92, 2005. doi:10.1093/molbev/msi103.

Drummond AJ, Suchard MA. Bayesian random local clocks, or one rate to rule them all. BMC biology. 2010 Dec;8(1):1-2. doi:10.1186/s12862-020-01609-4.

Fagundes De Carvalho LM. Statistical approaches to viral phylodynamics (Doctoral dissertation, University of Edinburgh). 2018. online.

Frankham R. Effective population size/adult population size ratios in wildlife: a review. Genetics Research. 1995 Oct;66(2):95-107. doi:10.1017/S0016672300034455.

Gavryushkina A, Welch D, Stadler T, Drummond AJ. Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration. PLoS computational biology. 2014 Dec 4;10(12):e1003919. doi:10.1371/journal.pcbi.1003919.

Gernhard, T. 2008. The conditioned reconstructed process. Journal of Theoretical Biology Volume 253, Issue 4, 21 August 2008, Pages 769-778 doi:10.1016/j.jtbi.2008.04.005.

Hasegawa M, Kishino H, Yano TA. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of molecular evolution. 1985 Oct;22(2):160-74. doi:10.1007/BF02101694.

Heled J, Drummond AJ. Calibrated tree priors for relaxed phylogenetics and divergence time estimation. Systematic biology. 2012 Jan 1;61(1):138-49. doi:10.1093/sysbio/syr087.

Heled J, Drummond AJ. Bayesian inference of population size history from multiple loci. BMC evolutionary biology. 2008 Dec;8(1):1-5. doi:10.1186/1471-2148-8-289.

Jenkins GM, Rambaut A, Pybus OG, Holmes EC. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. Journal of molecular evolution. 2002 Feb;54(2):156-65. doi:10.1007/s00239-001-0064-3

Kühnert D, Stadler T, Vaughan TG, Drummond AJ. Phylodynamics with migration: a computational framework to quantify population structure from genomic data. Molecular biology and evolution. 2016 Apr 9;33(8):2102-16. doi:10.1093/molbev/msw064.

Krasovec M, Rickaby RE, Filatov DA. Evolution of mutation rate in astronomically large phytoplankton populations. Genome biology and evolution. 2020 Jul 1. doi:10.1093/gbe/evaa131.

Kumar S, Subramanian S. Mutation rates in mammalian genomes. Proceedings of the National Academy of Sciences. 2002 Jan 22;99(2):803-8. doi:10.1073/pnas.022629899.

Lunn D, Jackson C, Best N, Thomas A, Spiegelhalter D. The BUGS book. A Practical Introduction to Bayesian Analysis, Chapman Hall, London. 2013.

Magallon S, Sanderson MJ. Absolute diversification rates in angiosperm clades. Evolution. 2001 Sep;55(9):1762-80. doi:10.1111/j.0014-3820.2001.tb00826.x.

Matschiner M, Musilová Z, Barth JM, Starostová Z, Salzburger W, Steel M, Bouckaert R. Bayesian phylogenetic estimation of clade ages supports trans-Atlantic dispersal of cichlid fishes. Systematic biology. 2017 Jan 1;66(1):3-22. doi:10.1093/sysbio/syw076.

Maturana PM, Brewer BJ, Klaere S, Bouckaert RR. Model selection and parameter inference in phylogenetics using Nested Sampling. Systematic biology. 2019 Mar 1;68(2):219-33. doi:10.1093/sysbio/syy050.

Müller NF, Bouckaert RR. Adaptive Metropolis-coupled MCMC for BEAST 2. PeerJ. 2020 Sep 16;8:e9473. doi:10.7717/peerj.9473.

Müller NF, Rasmussen D, Stadler T. MASCOT: parameter and state inference under the marginal structured coalescent approximation. Bioinformatics. 2018 Nov 15;34(22):3843-8. doi:10.1093/bioinformatics/bty406.

Ogilvie HA, Heled J, Xie D, Drummond AJ. Computational performance and statistical accuracy of *BEAST and comparisons with other methods. Systematic biology. 2016 May 1;65(3):381-96. doi:10.1093/sysbio/syv118.

Rosenberg MS, Subramanian S, Kumar S. Patterns of transitional mutation biases within and among mammalian genomes. Molecular biology and evolution. 2003 Jun 1;20(6):988-93. doi:10.1093/molbev/msg113.

Sanjuán R, Nebot MR, Chirico N, Mansky LM, Belshaw R. Viral mutation rates. Journal of virology. 2010 Oct 1;84(19):9733-48. doi:10.1128/JVI.00694-10.

Sarma A, Kay M. Prior setting in practice: Strategies and rationales used in choosing prior distributions for Bayesian analysis. Proceedings of the 2020 chi conference on human factors in computing systems 2020 Apr 21 (pp. 1-12). doi: 10.1145/3313831.3376377.

Shapiro B, Rambaut A, Drummond AJ. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Molecular biology and evolution. 2006 Jan 1;23(1):7-9. doi:10.1093/molbev/msj021.

Stadler T, Kühnert D, Bonhoeffer S, Drummond AJ. Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). Proceedings of the National Academy of Sciences. 2013 Jan 2;110(1):228-33. doi:10.1073/pnas.120796511.

Steel M, Mooers A. The expected length of pendant and interior edges of a Yule tree. Applied Mathematics Letters. 2010 Nov 1;23(11):1315-9. doi:10.1016/j.aml.2010.06.021.

Stoltz M, Baeumer B, Bouckaert R, Fox C, Hiscott G, Bryant D. Bayesian inference of species trees using diffusion models. Systematic Biology. 2021 Jan;70(1):145-61. doi:10.1093/sysbio/syaa051.

Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular biology and evolution. 1993 May 1;10(3):512-26. doi:10.1093/oxfordjournals.molbev.a040023.

Tavaré S, Balding DJ, Griffiths RC, Donnelly P. Inferring coalescence times from DNA sequence data. Genetics. 1997 Feb 1;145(2):505-18. doi:10.1093/genetics/145.2.505.

Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures on mathematics in the life sciences. 1986 Dec 31;17(2):57-86.

Waddell P. Evolutionary trees of apes and humans from DNA sequences. Handbook of human symbolic evolution. 1996:53-73.

Vaughan TG, Kühnert D, Popinga A, Welch D, Drummond AJ. Efficient Bayesian inference under the structured coalescent. Bioinformatics. 2014 Aug 15;30(16):2272-9. doi:10.1093/bioinformatics/btu201.

Yang J, Müller NF, Bouckaert R, Xu B, Drummond AJ. Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration. PLoS computational biology. 2019 Aug 6;15(8):e1007189. doi:10.1371/journal.pcbi.1007189.

Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. Journal of Molecular evolution. 1994 Sep;39(3):306-14. doi:10.1007/BF00160154.

Zhang R, Drummond A. Improving the performance of Bayesian phylogenetic inference under relaxed clock models. BMC evolutionary biology. 2020 Dec;20(1):1-28. doi:10.1186/s12862-020-01609-4.