<s>
In	O
bioinformatics	O
,	O
MAFFT	B-Application
(	O
for	O
multiple	O
alignment	O
using	O
fast	O
Fourier	O
transform	O
)	O
is	O
a	O
program	O
used	O
to	O
create	O
multiple	O
sequence	O
alignments	O
of	O
amino	O
acid	O
or	O
nucleotide	O
sequences	O
.	O
</s>
<s>
Published	O
in	O
2002	O
,	O
the	O
first	O
version	O
of	O
MAFFT	B-Application
used	O
an	O
algorithm	O
based	O
on	O
progressive	O
alignment	O
,	O
in	O
which	O
the	O
sequences	O
were	O
clustered	O
with	O
the	O
help	O
of	O
the	O
Fast	O
Fourier	O
Transform	O
.	O
</s>
<s>
Subsequent	O
versions	O
of	O
MAFFT	B-Application
have	O
added	O
other	O
algorithms	O
and	O
modes	O
of	O
operation	O
,	O
including	O
options	O
for	O
faster	O
alignment	O
of	O
large	O
numbers	O
of	O
sequences	O
,	O
higher	O
accuracy	O
alignments	O
,	O
alignment	O
of	O
non-coding	O
RNA	O
sequences	O
,	O
and	O
the	O
addition	O
of	O
new	O
sequences	O
to	O
existing	O
alignments	O
.	O
</s>
<s>
There	O
have	O
been	O
many	O
variations	O
of	O
the	O
MAFFT	B-Application
software	O
,	O
some	O
of	O
which	O
are	O
listed	O
below	O
:	O
</s>
<s>
MAFFT	B-Application
:	O
The	O
first	O
version	O
of	O
MAFFT	B-Application
,	O
created	O
by	O
Kazutaka	O
Katoh	O
in	O
2002	O
,	O
used	O
an	O
algorithm	O
based	O
on	O
progressive	O
alignment	O
,	O
in	O
which	O
the	O
sequences	O
were	O
clustered	O
with	O
the	O
help	O
of	O
the	O
Fast	O
Fourier	O
Transform	O
.	O
</s>
<s>
MAFFT	B-Application
v5	O
:	O
The	O
second	O
generation	O
of	O
the	O
MAFFT	B-Application
software	O
was	O
released	O
in	O
2005	O
and	O
was	O
a	O
rewrite	O
of	O
the	O
original	O
MAFFT	B-Application
software	O
.	O
</s>
<s>
MAFFT	B-Application
v6	O
:	O
The	O
third	O
generation	O
,	O
released	O
in	O
2006	O
,	O
again	O
improved	O
upon	O
the	O
previous	O
versions	O
.	O
</s>
<s>
MAFFT	B-Application
v7	O
:	O
The	O
fourth	O
generation	O
,	O
released	O
in	O
2012	O
,	O
improved	O
the	O
speed	O
and	O
accuracy	O
of	O
MAFFT	B-Application
substantially	O
.	O
</s>
<s>
The	O
MAFFT	B-Application
algorithm	O
works	O
following	O
these	O
5	O
steps	O
Pairwise	O
Alignment	O
,	O
Distance	O
Calculation	O
,	O
Guide	O
Tree	O
Construction	O
,	O
Progressive	O
Alignment	O
,	O
Iterative	O
Refinement	O
.	O
</s>
<s>
The	O
two	O
most	O
common	O
output	O
formats	O
are	O
pearson	O
/FASTA	O
and	O
Clustal	O
W/	O
CLUSTALW	B-Application
.	O
</s>
<s>
MAFFT	B-Application
is	O
a	O
multiple-sequence	O
alignment	O
algorithm	O
widely	O
regarded	O
as	O
one	O
of	O
the	O
most	O
accurate	O
and	O
versatile	O
tools	O
in	O
bioinformatics	O
.	O
</s>
<s>
One	O
of	O
the	O
key	O
strengths	O
of	O
MAFFT	B-Application
is	O
its	O
ability	O
to	O
handle	O
large	O
and	O
complex	O
datasets	O
,	O
including	O
sequences	O
with	O
high	O
degrees	O
of	O
divergence	O
.	O
</s>
<s>
Subsequent	O
versions	O
of	O
MAFFT	B-Application
have	O
added	O
other	O
algorithms	O
and	O
modes	O
of	O
operation	O
,	O
including	O
options	O
for	O
faster	O
alignment	O
of	O
large	O
numbers	O
of	O
sequences	O
,	O
higher	O
accuracy	O
alignments	O
,	O
alignment	O
of	O
non-coding	O
RNA	O
sequences	O
,	O
and	O
the	O
addition	O
of	O
new	O
sequences	O
to	O
existing	O
alignments	O
.	O
</s>
<s>
Moreover	O
,	O
MAFFT	B-Application
offers	O
various	O
alignment	O
methods	O
and	O
strategies	O
,	O
including	O
iterative	O
refinement	O
and	O
consistency-based	O
approaches	O
,	O
which	O
further	O
improve	O
the	O
accuracy	O
and	O
robustness	O
of	O
the	O
alignments	O
.	O
</s>
<s>
With	O
its	O
high	O
accuracy	O
,	O
versatility	O
,	O
and	O
range	O
of	O
features	O
,	O
MAFFT	B-Application
is	O
a	O
powerful	O
tool	O
for	O
multiple	O
sequence	O
alignment	O
,	O
widely	O
used	O
and	O
appreciated	O
by	O
the	O
scientific	O
community	O
.	O
</s>
