mafft

Multiple sequence alignment tool using fast Fourier transforms

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Multiple alignments with fast Fourier transforms

mafft

Align sequences from a FASTA file with default parameters$ mafft input.fasta > output.fasta

Perform high-accuracy alignment using iterative refinement$ mafft --maxiterate 1000 --localpair input.fasta > output.fasta

Quick alignment suitable for large datasets$ mafft --retree 1 --maxiterate 0 input.fasta > output.fasta