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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)

THIS MANUAL IS FOR V6.2XX (2007) | NAME | SYNOPSIS | DESCRIPTION | OPTIONS | FILES | ENVIONMENT | SEE ALSO | REFERENCES | AUTHORS | COPYRIGHT

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