This command unlinks model parameters across partitions of the data. The correct usage is:
unlink <parameter name> = (<all> or <partition list>)
A little background is necessary to understand this command. Upon execution of a file, a default partition is set up. This partition referenced either by its name ("default") or number (0). If your data are all of one type, then this default partition does not actually divide up your characters. However, if your datatype is mixed, then the default partition contains as many divisions as there are datatypes in your character matrix. Of course, you can also define other partitions, and switch among them using the set command ("set partition=<name/number>"). Importantly, you can also assign model parameters to individual partitions or to groups of them using the "applyto" option in lset and prset. When the program attempts to perform an analysis, the model is set for individual partitions. If the same parameter applies to different partitions and if that parameter has the same prior, then the program will link the parameters: that is, it will use a single value for the parameter. The program's default, then, is to strive for parsimony. However, there are lots of cases where you may want unlink a parameter across partitions. For example, you may want a different transition/transversion rate ratio to apply to different partitions. This command allows you to unlink the parameters, or to make them different across partitions. The converse of this command is "link", which links together parameters that were previously told to be different. The list of parameters that can be unlinked includes:
Tratio -- Transition/transversion rate ratio
Revmat -- Substitution rates of GTR model
Omega -- Nonsynonymous/synonymous rate ratio
Statefreq -- Character state frequencies
Shape -- Gamma shape parameter
Pinvar -- Proportion of invariable sites
Correlation -- Correlation parameter of autodiscrete gamma
Switchrates -- Switching rates for covarion model
Brlens -- Branch lengths of tree
Topology -- Topology of tree
Speciationrates -- Speciation rates for birth-death process
Extinctionrates -- Extinction rates for birth-death process
Theta -- Parameter for coalescence process
Growthrate -- Growth rate of coalesence process
For example,
unlink shape=(all)
unlinks the gamma shape parameter across all partitions of the data. You can use "showmodel" to see the current linking status of the characters.