See also
  Phylogenetic trees are NOT good guide trees!

The –usetree option allows you to provide your own guide tree. For example,

  muscle -in seqs.fa -out seqs.afa -usetree mytree.phy

The tree must by in Newick format, as used by the Phylip package.

You will get a warning if you use the –usetree option, to make sure that you are aware that usually, phylogenetic trees are not good guide trees. To disable the warning, use –usetree_nowarn instead, e.g.:

  muscle -in seqs.fa -out seqs.afa -usetree_nowarn mytree.phy