Muscle

MUSCLE is one of the most common tools to align sequences. In most cases, only a few command line options are needed.

Make an alignment and save to a file in FASTA format:

  muscle -in seqs.fa -out seqs_muscle.afa

Write alignment to the console in CLUSTALW format (more readable than FASTA):

  muscle -in seqs.fa -clw

If you have an existing alignment, you can add a new sequence using the following:

   muscle -profile -in1 existing_msa.afa -in2 new_seq.fa -out combined.afa

If you have more than one new sequence you need to align them first, and then can merge the two alignments:

  muscle -in new_seqs.fa -out new_seqs.afa

  muscle -profile -in1 existing_aln.afa -in2 new_seqs.afa -out combined.afas

Commandline muscle is very helpful for making quick trees. Depending on the depth of phylogenetics needed, a simple NJ tree maybe all you need.

Make a UPGMA tree from a multiple alignment:

 muscle -maketree -in seqs_muscle.afa -out seqs_muscle_tree.phy

Make a Neighbor-Joining tree from a multiple alignment:

  muscle -maketree -in seqs_muscle.afa -out seqs_muscle_tree.phy -cluster neighborjoining