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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 --blobalpair, --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.  Deafult: 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.  Deafult: 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.  Deafult: auto

       --amino
           Assume the sequences are amino acid.  Deafult: 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 <katoh_at_bioreg.kyushu-u.ac.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.