# The `--config` command:

-c       <file>                              Config file to read.
--config <file>

Read inference options and model-language definitions from <file>.
This can be useful for recording and re-running an analysis.

A scalar option on the command line overrides the value in <file>.
Repeated options are combined, with command-line values first.

Each option `--option <value>` is given on its own line using the
syntax `:option value`.  A value may be blank for a flag.

Blank lines and lines whose first non-whitespace character is `#`
are ignored.  Every other line is model-language source.  Source
lines may appear before, between, or after option lines.  Sequence
data is specified with `:align`.

# Example command:

   bali-phy --config=script --name=ITS

# Example script:

   # Compute probability and exit.
   :test

   # Sequence data for the three partitions.
   :align ITS1.fasta
   :align 5.8S.fasta
   :align ITS2.fasta

   # Link the first and third partition's smodel.
   :smodel 1,3:TN93+>ASRV.Free(n=3)

   # The second partition has a fixed alignment.
   :smodel 2:TN93
   :imodel 2:none

   # Link the first and third partition's scale.
   :scale 1,3:
