Multiple alignment program for amino acid or nucleotide sequences
Recent versions (v7.1xx; 2013 Jan.) have more features than those described below. See also the tips page at http://mafft.cbrc.jp/alignment/software/tips0.html
mafft [options] input [> output] linsi input [> output] ginsi input [> output] einsi input [> output] fftnsi input [> output] fftns input [> output] nwns input [> output] nwnsi input [> output] mafft-profile group1 group2 [> output]
input, group1 and group2 must be in FASTA format.
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods.
\h'-04'•\h'+03'L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information): mafft --localpair --maxiterate 1000 input [> output] linsi input [> output]
\h'-04'•\h'+03'G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information): mafft --globalpair --maxiterate 1000 input [> output] ginsi input [> output]
\h'-04'•\h'+03'E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences): mafft --ep 0 --genafpair --maxiterate 1000 input [> output] einsi input [> output]
For E-INS-i, the --ep 0 option is recommended to allow large gaps.
\h'-04'•\h'+03'FFT-NS-i (iterative refinement method; two cycles only): mafft --retree 2 --maxiterate 2 input [> output] fftnsi input [> output]
\h'-04'•\h'+03'FFT-NS-i (iterative refinement method; max. 1000 iterations): mafft --retree 2 --maxiterate 1000 input [> output]
\h'-04'•\h'+03'FFT-NS-2 (fast; progressive method): mafft --retree 2 --maxiterate 0 input [> output] fftns input [> output]
\h'-04'•\h'+03'FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree): mafft --retree 1 --maxiterate 0 input [> output]
\h'-04'•\h'+03'NW-NS-i (iterative refinement method without FFT approximation; two cycles only): mafft --retree 2 --maxiterate 2 --nofft input [> output] nwnsi input [> output]
\h'-04'•\h'+03'NW-NS-2 (fast; progressive method without the FFT approximation): mafft --retree 2 --maxiterate 0 --nofft input [> output] nwns input [> output]
\h'-04'•\h'+03'NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm): mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
mafft-profile group1 group2 [> output]
or:
mafft --maxiterate 1000 --seed group1 --seed group2 /dev/null [> 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.
Mafft stores the input sequences and other files in a temporary directory, which by default is located in /tmp.
MAFFT_BINARIES
Indicates the location of the binary files used by mafft. By default, they are searched in /usr/local/lib/mafft, but on Debian systems, they are searched in /usr/lib/mafft.
FASTA_4_MAFFT
This variable can be set to indicate to mafft the location to the fasta34 program if it is not in the PATH.
\h'-04'•\h'+03'Katoh and Toh (Bioinformatics 23:372-374, 2007) PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences (describes the PartTree algorithm).
\h'-04'•\h'+03'Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment (describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies)
\h'-04'•\h'+03'Katoh, Misawa, Kuma and Miyata (Nucleic Acids Res. 30:3059-3066, 2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform (describes the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies)
\h'-04'•\h'+03'Katoh and Misawa (Seibutsubutsuri 46:312-317, 2006) Multiple Sequence Alignments: the Next Generation
\h'-04'•\h'+03'Katoh and Kuma (Kagaku to Seibutsu 44:102-108, 2006) Jissen-teki Multiple Alignment
Kazutaka Katoh <kazutaka.katoh_at_aist.go.jp>
Wrote Mafft.
Charles Plessy <charles-debian-nospam_at_plessy.org>
Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template.
Copyright © 2002-2007 Kazutaka Katoh (mafft)
Copyright © 2007 Charles Plessy (this manpage)
Mafft and its manpage are offered under the following conditions:
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