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MAFFT(1) Mafft Manual MAFFT(1)
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:
o 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]
o 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]
o 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:
o FFT-NS-i (iterative refinement method; two cycles only):
mafft --retree 2 --maxiterate 2 input [> output]
fftnsi input [> output]
o FFT-NS-i (iterative refinement method; max. 1000 iterations):
mafft --retree 2 --maxiterate 1000 input [> output]
o FFT-NS-2 (fast; progressive method):
mafft --retree 2 --maxiterate 0 input [> output]
fftns input [> output]
o FFT-NS-1 (very fast; recommended for >2000 sequences; progressive
method with a rough guide tree):
mafft --retree 1 --maxiterate 0 input [> output]
o NW-NS-i (iterative refinement method without FFT approximation; two
cycles only):
mafft --retree 2 --maxiterate 2 --nofft input [> output]
nwnsi input [> output]
o NW-NS-2 (fast; progressive method without the FFT approximation):
mafft --retree 2 --maxiterate 0 --nofft input [> output]
nwns input [> output]
o 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
o 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).
o 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)
o 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
o Katoh and Misawa (Seibutsubutsuri 46:312-317, 2006) Multiple
Sequence Alignments: the Next Generation
o 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 (C) 2002-2007 Kazutaka Katoh (mafft)
Copyright (C) 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.
mafft 6.240 2007-06-09 MAFFT(1)