BEAST 2 Help Me Choose

BEAST 2 Help Me Choose

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

Priors


Birth rate prior
Calibrated Yule birth rate prior
Clock 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
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


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Bayesian evolutionary analysis by sampling trees

Disclaimer: The above is the opinion of the author RB. If you do not agree, or spot a mistake, contact the author, or discuss this in the issues area or raise a new issue. A link will be added from this page to make sure others can find it.

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