MAFFT version 6

Multiple alignment program for amino acid or nucleotide sequences

If you have ∼10 protein sequences that are distantly related to each other, the alignment accuracy can be further improved by the use of homologs;

  1. collect a number (>20) of homologs of the sequences,
  2. align them all together using L-INS-i,
  3. and then remove the homologs. 
This process is automatically done on the MAFFT server at CBRC when the 'Mafft-homologs' option is selected. 
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