Provided by: mafft_7.505-1_amd64 
THIS MANUAL IS FOR V6.2XX (2007)
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
NAME
mafft - Multiple alignment program for amino acid or nucleotide sequences
SYNOPSIS
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.
DESCRIPTION
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers
a range of multiple alignment methods.
Accuracy-oriented methods:
• 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]
• 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]
• 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.
Speed-oriented methods:
• FFT-NS-i (iterative refinement method; two cycles only):
mafft --retree 2 --maxiterate 2 input [> output]
fftnsi input [> output]
• FFT-NS-i (iterative refinement method; max. 1000 iterations):
mafft --retree 2 --maxiterate 1000 input [> output]
• FFT-NS-2 (fast; progressive method):
mafft --retree 2 --maxiterate 0 input [> output]
fftns input [> output]
• FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough
guide tree):
mafft --retree 1 --maxiterate 0 input [> output]
• NW-NS-i (iterative refinement method without FFT approximation; two cycles only):
mafft --retree 2 --maxiterate 2 --nofft input [> output]
nwnsi input [> output]
• NW-NS-2 (fast; progressive method without the FFT approximation):
mafft --retree 2 --maxiterate 0 --nofft input [> output]
nwns input [> output]
• 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]
Group-to-group alignments
mafft-profile group1 group2 [> output]
or:
mafft --maxiterate 1000 --seed group1 --seed group2 /dev/null [> output]
OPTIONS
Algorithm
--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
Parameter
--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
Output
--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
Input
--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.
FILES
Mafft stores the input sequences and other files in a temporary directory, which by
default is located in /tmp.
ENVIONMENT
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.
SEE ALSO
mafft-homologs(1)
REFERENCES
In English
• 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).
• 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)
• 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)
In Japanese
• Katoh and Misawa (Seibutsubutsuri 46:312-317, 2006) Multiple Sequence Alignments: the
Next Generation
• Katoh and Kuma (Kagaku to Seibutsu 44:102-108, 2006) Jissen-teki Multiple Alignment
AUTHORS
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
Copyright © 2002-2007 Kazutaka Katoh (mafft)
Copyright © 2007 Charles Plessy (this manpage)
Mafft and its manpage are offered under the following conditions:
Redistribution and use in source and binary forms, with or without modification, are
permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this list of
conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice, this list
of conditions and the following disclaimer in the documentation and/or other materials
provided with the distribution.
3. The name of the author may not be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF
THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.