# The `--set` command:

--set <key>=<value>                         Set configuration value.

Pass a key-value pair into BAli-Phy.  The <value> is a json value.

# Examples:

   # Work twice at hard at resampling the alignment (default: 1.0)
   bali-phy dna.fasta --set alignment-sampling-factor=2.0

   # Write the alignment every 10th logged iteration (default: 10)
   bali-phy dna.fasta --set alignment-extra-subsample=10

   # Infer ambiguous characters for leaf sequences (default: false)
   bali-phy dna.fasta -I none --set infer-ambiguous-observed=true

   # Write fixed alignments (useful for ancestral sequence reconstruction) (default: false)
   bali-phy dna.fasta -I none --set write-fixed-alignments=true

   # Stop enforcing low gap probabilities after 10 iterations (default: 10)
   bali-phy dna.fasta --set alignment-burnin=10

   # Disallow site-compression (default: true)
   bali-phy dna.fasta -I none --set site-compression=false

# See:

   initial-value
