Make a UPGMA tree from a multiple alignment:

 muscle -maketree -in seqs.afa -out seqs.phy

Make a Neighbor-Joining tree from a multiple alignment:

  muscle -maketree -in seqs.afa -out seqs.phy -cluster neighborjoining

UPGMA or Neighbor joining?
Neighbor-joining trees will usually be a better estimate of the true phylogenetic tree. UPGMA is faster, which can be useful with large datasets when N-J is too slow.

Input file
Specified using the -in option. Must be in aligned FASTA format.

Output file
Specified using the -out option. The tree is written in Newick format, which is supported by most phylogenetic analysis packages such as PHYLIP. See also this article on the Newick format in the PHYLIP documentation.