# The `--smodel` command:

-S       [partitions:]<model>               Substitution model.
--smodel [partitions:]<model>

If no model is specified for a partition, then a default model is chosen
based on the alphabet for that partition.  The defaults are:

   DNA        -> TN
   RNA        -> TN
   AminoAcids -> LG
   Triplets   -> TN+x3
   Codons     -> M0

Many substitution models have parameters that can be specified.  For
example the HKY model has an optional kappa parameter.  Optional
parameters have default priors.  For example HKY defaults to:

   HKY[kappa~logNormal[log[2],0.25]]

See help on "parameters" for information on specifying priors or values.

If no partitions are specified, then every partition gets a separate
(unlinked) copy of the model.

If partitions are specified, then the partitions are linked. That is,
they share the same parameter values as well as the same model.

The --smodel command can be given multiple times, but the same
partition cannot be referenced twice.

# Examples:

   -S HKY
   
   --smodel=HKY
   
   -S GTR+Rates.Gamma+INV
   
   -S 1,3:HKY+Rates.Gamma[n=4]+INV -S 2:LG+Rates.Gamma+INV
   
In the last example, the substitution models of partitions 1 and 3 are linked.

# See also:

   parameters, priors, HKY, GTR, Rates.Gamma, INV
