BEAST 2 Help Me Choose

BEAST 2 Help Me Choose Wilson Balding operator

Wilson Balding operator

Implements the unweighted Wilson-Balding branch swapping move (Drummond et al, 2002). This move is similar to one proposed by WILSON and BALDING 1998 and involves removing a subtree and re-attaching it on a new parent branch. See picture.

markclades (Boolean)

Mark all ancestors of nodes changed by the operator as changed, up to the MRCA of all nodes changed by the operator (optional, default: false). This option is used when a Pruned Tree (BEASTLabs) is included in the analyses, and can be left false for Standard template analyses.

weight (Double)

Weight with which this operator is selected (required). See also operator weight tuning.

Wilson Balding is useful during burn-in, but later on during MCMC tends to have low acceptance rate, so the weight is usually set low.

References

Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics. 2002 Jul 1;161(3):1307-20. doi:/10.1093/genetics/161.3.1307.

Bayesian evolutionary analysis by sampling trees

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