MUSCLE manual > tree output files
Guide tree output files
See also
  Using a precomputed guide tree
  Making a N-J or UPGMA tree from a multiple alignment

You can save the guide tree from the first and/or second iteration using the -tree1 and -tree2 options, e.g.:

muscle -in seqs.fa -out seqs.afa -tree1 first.phy -tree2 second.phy

The trees are saved in Newick (PHYLIP-compatible) format.

These should not be considered high-quality phylogenetic trees, though they may be useful as a fast way to get approximate evolutionary relationships between some new sequences:

   muscle -in seqs.fa -out seqs.afa -tree1 first.phy -maxiters 1

You can make a neighbor-joining tree if you want a better estimate of the true phylogeny.