This command links model parameters across partitions of the data. The correct usage is:
link <parameter name> = (<all> or <partition list>)
The list of parameters that can be linked 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 coalesence process
Growthrate -- Growth rate of coalesence process
For example,
link shape=(all)
links the gamma shape parameter across all partitions of the data. You can use "showmodel" to see the current linking status of the characters. For more information on this command, see the help menu for links converse, unlink ("help unlink");