mafft

Multiple alignment program for amino acid or nucleotide sequences

Description

MAFFT is a multiple sequence alignment program which offers three accuracy-oriented methods:

* L-INS-i (probably most accurate; recommended for <200 sequences;

iterative refinement method incorporating local pairwise alignment

information),

* G-INS-i (suitable for sequences of similar lengths; recommended for

<200 sequences; iterative refinement method incorporating global

pairwise alignment information),

* E-INS-i (suitable for sequences containing large unalignable regions;

recommended for <200 sequences),

and five speed-oriented methods:

* FFT-NS-i (iterative refinement method; two cycles only),

* FFT-NS-i (iterative refinement method; max. 1000 iterations),

* FFT-NS-2 (fast; progressive method),

* FFT-NS-1 (very fast; recommended for >2000 sequences; progressive

method with a rough guide tree),

* NW-NS-PartTree-1 (recommended for ∼50,000 sequences; progressive

method with the PartTree algorithm).

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