cbrc
MAFFT version 7

Multiple alignment program for amino acid or nucleotide sequences

--addfull and --add: Adding unaligned full-length sequence(s) into an existing alignment

--add --add
% mafft --add new_sequences --reorder existing_alignment > output

--addfragments: Adding unaligned fragmentary sequence(s) into an existing alignment New!

--add --addfragments

Accurate option:

% mafft --addfragments fragments --reorder --thread -1 existing_alignment > output
Fast option (accurate enough for highly similar sequences):
% mafft --addfragments fragments --reorder --6merpair --thread -1 existing_alignment > output
BUG!! Bug information: Versions 6.923 - 6.950 had a bug in the combination of --addfragments and --reorder.  The order of sequences in the output was incorrect.  This bug has been fixed in version 6.951 (2012/Oct/18).
BUG!! Bug information: Versions ≤6.815 had a problem in processing partial sequences.  When the new sequence has domains A and B but a part of sequences in the existing alignment lack domain B, domain B was sometimes not aligned.  This problem has been fixed in version 6.817 (2010/Aug/14).

Possible misalignment by versions ≤6.815:
existing alignment: AAAAAAAA---------BBBBBBBBB
existing alignment: AAAAAAAA---------BBBBBBBBB
existing alignment: AAAAAAAA------------------
new sequence:       AAAAAAAABBBBBBBBB---------

Fixed in versions ≥6.817:

existing alignment: AAAAAAAABBBBBBBBB
existing alignment: AAAAAAAABBBBBBBBB
existing alignment: AAAAAAAA---------
new sequence:       AAAAAAAABBBBBBBBB

Adding aligned sequences (profile) into an existing alignment

% mafft --addprofile aligned_sequences existing_alignment > output

Difference from the --seed option

--seed

Difference from the mafft-profile program

The --addprofile option covers all the situations where the mafft-profile program was used.  Morever, the former is applicable to larger datasets than the latter.  Therefore, the mafft-profile program will be deleted in future releases. 

The mafft-profile program assumes that each profile separately forms a monophyletic cluster.
mafft-profile