fftns

Langue: en

Autres versions - même langue

Version: 2008\-09\-01 (debian - 07/07/09)

Section: 1 (Commandes utilisateur)

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]
mafft-profile group1 group2 [> output]

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-PartTree-1 (recommended for ?50,000 sequences; progressive method with the PartTree algorithm):
mafft --retree 1 --maxiterate 0 --parttree input [> output]

Group-to-group alignments

mafft-profile group1 group2 [> output]
or:
mafft --maxiterate 1000 --seed group1 --seed group2 /dev/null [> output]

OPTIONS

--auto

--clustalout

--reorder

--inputorder

--algq

--groupsize

--partsize

--parttree

--dpparttree

--fastaparttree

--treeout

--fastswpair

--fastapair

--noscore

--6merpair

--blastpair

--globalpair

--localpair

--genafpair

--memsave

--nuc

--amino

--fft

--nofft

--quiet

--coreext

--core

--maxiterate

--retree

--aamatrix

--fmodel

--jtt

--tm

--bl

--weighti

--op

--ep

--lop

--LOP

--lep

--lexp

--LEXP

--corethr

--corewin

--seed

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 (???? 46:312-317, 2006) Multiple Sequence Alignments: the Next Generation
•Katoh and Kuma (????? 44:102-108, 2006) Jissen-teki Multiple Alignment

DIVERGENCE FROM UPSTREAM

mafft-homologs has been patched to enhance the security of the temporary files it creates. You can consult the patch in the Debian source package. It has been reviewed and amended by Kazutaka Katoh, the upstream author of MAFFT.

AUTHORS

Kazutaka Katoh <katoh_at_bioreg.kyushu-u.ac.jp.>

Wrote Mafft.

Charles Plessy <charles-debian-nospam@plessy.org>

Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template.
Copyright © 2002, 2003, 2004, 2005, 2006, 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.