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.