# The `--pre-burnin` command:

--pre-burnin <number>                       Number of pre-burnin iterations.

BAli-Phy performs a few iterations of MCMC to estimate the
tree only before starting full MCMC inference of alignment,
tree, and parameters.  If the initial alignment is good
but the initial tree is bad, MCMC may unalign all the sequences
and lose the good alignment.  Estimating the tree before
allowing the alignment to vary avoids this situation.

The pre-burnin consists of a few stages:

1. Estimate the scale-factor for each partition.
2. Estimate the tree using an SPR for each branch.
3. Estimate the tree using an NNI for each branch.

The second stage can be quite slow for large trees, so `bali-phy`
only performs 1 iteration.  For the first and third stage, <number>
iterations are performed, defaulting to 3 if not specified.

Specifying a value of 0 disables pre-burnin.

# Examples:

   # The default.
   bali-phy dna.fasta --pre-burnin=3

   # Only do one round of SPR.
   bali-phy dna.fasta --pre-burnin=1

   # Disable pre-burnin
   bali-phy dna.fasta --pre-burnin=0
