# The `--set` command:

--set <key>=<value>                         Initialize parameter value.

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

# Examples:

   # Work twice at hard at resampling the alignment.
   bali-phy dna.fasta --set alignment\_sampling\_factor=2.0

   # Write fixed alignments (for ancestral sequence reconstruction)
   bali-phy dna.fasta -I none --set write\_fixed_alignments=true

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

   # Disallow site-compression
   bali-phy dna.fasta -I none --set compression=false
