MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
mafft [arguments] input > output
--auto
Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2)
--6merpair
Distance is calculated based on the number of shared 6mers. Default: on
--globalpair
All pairwise alignments are computed with the Needleman-Wunsch algorithm. More accurate but slower than --6merpair. Suitable for a set of globally alignable sequences. Applicable to up to ~200 sequences. A combination with --maxiterate 1000 is recommended (G-INS-i). Default: off (6mer distance is used)
--localpair
All pairwise alignments are computed with the Smith-Waterman algorithm. More accurate but slower than --6merpair. Suitable for a set of locally alignable sequences. Applicable to up to ~200 sequences. A combination with --maxiterate 1000 is recommended (L-INS-i). Default: off (6mer distance is used)
--genafpair
All pairwise alignments are computed with a local algorithm with the generalized affine gap cost (Altschul 1998). More accurate but slower than --6merpair. Suitable when large internal gaps are expected. Applicable to up to ~200 sequences. A combination with --maxiterate 1000 is recommended (E-INS-i). Default: off (6mer distance is used)
--fastapair
All pairwise alignments are computed with FASTA (Pearson and Lipman 1988). FASTA is required. Default: off (6mer distance is used)
--weighti number
Weighting factor for the consistency term calculated from pairwise alignments. Valid when either of --globalpair, --localpair, --genafpair, --fastapair or --blastpair is selected. Default: 2.7
--retree number
Guide tree is built number times in the progressive stage. Valid with 6mer distance. Default: 2
--maxiterate number
number cycles of iterative refinement are performed. Default: 0
--fft
Use FFT approximation in group-to-group alignment. Default: on
--nofft
Do not use FFT approximation in group-to-group alignment. Default: off
--noscore
Alignment score is not checked in the iterative refinement stage. Default: off (score is checked)
--memsave
Use the Myers-Miller (1988) algorithm. Default: automatically turned on when the alignment length exceeds 10,000 (aa/nt).
--parttree
Use a fast tree-building method (PartTree, Katoh and Toh 2007) with the 6mer distance. Recommended for a large number (> ~10,000) of sequences are input. Default: off
--dpparttree
The PartTree algorithm is used with distances based on DP. Slightly more accurate and slower than --parttree. Recommended for a large number (> ~10,000) of sequences are input. Default: off
--fastaparttree
The PartTree algorithm is used with distances based on FASTA. Slightly more accurate and slower than --parttree. Recommended for a large number (> ~10,000) of sequences are input. FASTA is required. Default: off
--partsize number
The number of partitions in the PartTree algorithm. Default: 50
--groupsize number
Do not make alignment larger than number sequences. Valid only with the --*parttree options. Default: the number of input sequences
--op number
Gap opening penalty at group-to-group alignment. Default: 1.53
--ep number
Offset value, which works like gap extension penalty, for group-to-group alignment. Default: 0.123
--lop number
Gap opening penalty at local pairwise alignment. Valid when the --localpair or --genafpair option is selected. Default: -2.00
--lep number
Offset value at local pairwise alignment. Valid when the --localpair or --genafpair option is selected. Default: 0.1
--lexp number
Gap extension penalty at local pairwise alignment. Valid when the --localpair or --genafpair option is selected. Default: -0.1
--LOP number
Gap opening penalty to skip the alignment. Valid when the --genafpair option is selected. Default: -6.00
--LEXP number
Gap extension penalty to skip the alignment. Valid when the --genafpair option is selected. Default: 0.00
--bl number
BLOSUM number matrix (Henikoff and Henikoff 1992) is used. number=30, 45, 62 or 80. Default: 62
--jtt number
JTT PAM number (Jones et al. 1992) matrix is used. number>0. Default: BLOSUM62
--tm number
Transmembrane PAM number (Jones et al. 1994) matrix is used. number>0. Default: BLOSUM62
--aamatrix matrixfile
Use a user-defined AA scoring matrix. The format of matrixfile is the same to that of BLAST. Ignored when nucleotide sequences are input. Default: BLOSUM62
--fmodel
Incorporate the AA/nuc composition information into the scoring matrix. Default: off
--clustalout
Output format: clustal format. Default: off (fasta format)
--inputorder
Output order: same as input. Default: on
--reorder
Output order: aligned. Default: off (inputorder)
--treeout
Guide tree is output to the input.tree file. Default: off
--quiet
Do not report progress. Default: off
--nuc
Assume the sequences are nucleotide. Default: auto
--amino
Assume the sequences are amino acid. Default: auto
--seed alignment1 [--seed alignment2 --seed alignment3 ...]
Seed alignments given in alignment_n (fasta format) are aligned with sequences in input. The alignment within every seed is preserved.