# The `--iterations` command:

-i           <number>                       Number of MCMC iterations.
--iterations <number>

BAli-Phy resamples every parameter and every pairwise alignment
during each iteration, as well as performing an NNI topology proposal
across each internal branch.  Iteration numbers in BAli-Phy may
therefore be lower that other software which changes only one
parameter per iteration.

BAli-phy doesn't use a stopping rule, so you need to diagnose
convergence and stop the MCMC yourself.

If you know how many iterations of MCMC you want, then this option
allows stopping the MCMC after <number> iterations.

To avoid forgotten jobs consuming infinite CPU resources on a shared
computing cluster, MCMC will stop after 200,000 iterations if the
maximum number of iterations is not specified.

# Examples:

   # Stop after 4000 iterations
   bali-phy dna.fasta -i 4000

   # Don't stop after 200000 iterations:
   bali-phy dna.fasta --iter=100000000000
