# The `--disable` command:

--disable <moves>                           Disable MCMC moves.

Disable some MCMC moves, provided as a comma-separated list.
This can be useful to hold the tree fixed.

A hierarchy of MCMC moves, along with whether they are enabled
or disabled, is displayed in the file `C1.out`. 
These moves can be enabled or disabled by name or attribute.

MCMC moves have attributes that be used to disable them:

 * topology:         changes the topology
 * lengths:          changes the branch lengths
 * alignment:        changes the alignment
 * alignment\_branch: change the alignment of leaf sequences

This allows one to fix the topology by writing `--disable=topology`.

# Examples:

   # Fix the topology
   bali-phy dna.fasta --tree=newick.tree --disable=topology

   # Fix the topology and *relative* branch lengths
   bali-phy dna.fasta --tree=newick.tree --disable=tree

   # Fix the topology and branch lengths
   bali-phy dna.fasta --tree=newick.tree --disable=tree --scale=1

   # Disable SPR
   bali-phy dna.fasta --disable=SPR

# See also:

   enable
