# The `--config` command:

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

Read command-line options from <file>.  This can be useful for
recording the options used in an analysis and re-running analyses.

Any other command line options will be added after the ones read
from <file>.

Each option `--command <value>" is given on its own line using the
syntax `command = value`.  If the option does not take a value then
write just `command =`.

Comments begin with `#`, and blank lines are allowed.  Sequence
data is specified using the command `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+>Rates.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:
