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PROGRAM:

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.

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