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einsi - Online in the Cloud

Run einsi in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command einsi that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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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