Multiple alignment program for amino acid or nucleotide sequences

Tips

• How to install MAFFT without being root
• Building an MSA from partial MSA(s) and unaligned sequences
  • --seed
  • --add, --addfragments, --addprofile
  • --merge
  • Regional re-alignment
• MAFFT alignments are TOO LONG!
• The difference between a default parameter of old versions (--ep 0.123) and that of the current version (--ep 0.0)
• Running MAFFT with a small (<∼4GB) RAM
• Running MAFFT efficiently with a large (>∼8GB) RAM
• How to select an appropriate strategy for a relatively small (up to ∼200 sequences × ∼5,000 residues) sequence alignment
• Adding homologs to improve alignment accuracy
• Incorporating protein structural information to improve alignment accuracy Beta version
• Multiple alignment of diverged ncRNA sequences with predicted structural information
• How to align large data
• Full-length MSA of closely-related viral genomes (2020/Apr)  Experimental
• How to get all-to-all pairwise alignments, instead of a multiple alignment
• How to get a distance matrix, instead of alignment
• How to get a guide tree or a rough clustering
• How to give a user-defined guide tree
• Adjusting parameters for an alignment of closely related DNA sequences
• Preserving uppercase/lowercase
• Unusual characters (U, O, !, @, #, etc.) in biological sequence
• Non-biological sequences (2017/Dec)
• How to give a user-defined scoring matrix
• How to select sequences to be included into an MSA
• Post processing
• How to convert a tree to the PDF or PNG format in the online service
• Codon-based alignment or DNA alignment based on translated protein sequences
• Multithreading
• Permission error in stderr
• If opposite strand sequences are included?
• Is there a stable (non-beta) release?
• Where are previous versions? → Please send request using feedback form.
• How to cite MAFFT
• ...