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
upper bounds can be defined.
Lower and upper bounds are usually provided through the BEAUti template and have sensible values most of the time.
value entry can be used to provide a sensible starting value.
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.
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.
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.