# Setting parameter values:

Models, functions and probability distributions all take named
parameters in BAli-Phy. Parameters are in given square brackets:

   Model[parameter1=value,parameter2~distribution]

Values are given with `=`, and priors are given with `~`.
A value or prior for a parameter must be given, unless the
model or function has a default value specified.

For example, the Tamura-Nei (TN) model has 2 parameters, `kappaPur`
and `kappaPyr`, with default priors.  Thus the following are the same:

     TN
     TN[kappaPur~logNormal[log[2],0.5],kappaPyr~logNormal[log[2],0.5]] 

It is also possible to specify parameter values by position only:

     TN[2,~logNormal[log[1],0.5]]

The parameter names, order, type and default value for any function
can be found by giving that function name to the `--help` command.
For example `bali-phy --help=TN` or `bali-phy help TN` give
information on the TN model.

# See also:

   priors
