Multiple alignment
muscle -in in.fasta -out out.afa
# output format - Clustal style
muscle -in in.fasta -out out.fasta -clw
# quick alignment - only two iterations
muscle -in seqs.fa -out seqs.afa -maxiters 2
# clustering
muscle -cluster -in seqs.fa -tree1 tree.phy
References
Manual
http://www.drive5.com/muscle/muscle.html