# 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        -> tn93
   RNA        -> tn93
   AminoAcids -> lg08
   Triplets   -> tn93+>x3
   Codons     -> gy94

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 hky85 defaults to:

   hky85(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 hky85
   
   --smodel=hky85
   
   -S 'gtr +> Rates.gamma +> inv'
   
   -S '1,3:hky85 +> Rates.gamma(n=4) +> inv' -S '2:lg08 +> Rates.gamma +> inv'
   
In the last example, the substitution models of partitions 1 and 3 are linked.

# See also:

   parameters, priors, hky85, gtr, Rates.gamma, inv
