BEAST 2 Help Me Choose

BEAST 2 Help Me Choose Standard template -- initialization panel

Standard template – initialization panel

The initialisation panel allows you to set starting values for all state nodes, usually parameters and the tree.

For parameters, the lower and upper bounds can be defined. Lower and upper bounds are usually provided through the BEAUti template and have sensible values most of the time.

The value entry can be used to provide a sensible starting value.

The dimension entry determines the dimension of the parameter, which is most often 1, but for frequencies it is 4 for nucleotide data, and 20 for amino acid data.

The minor-dimension entry is used for two-dimensional parameters and specifies the size of the minor dimension. A minor dimension of 1 indicates it is just an array. This entry can usually be left to its default value.

The estimate should be left checked. If not checked, the parameter is removed from the state and will be kept constant throughout the MCMC.

See also starting tree panel for alternative ways to initialis the tree.

Bayesian evolutionary analysis by sampling trees

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