<s>
MUltiple	B-Application
Sequence	I-Application
Comparison	I-Application
by	I-Application
Log-Expectation	I-Application
(	O
MUSCLE	O
)	O
is	O
computer	O
software	O
for	O
multiple	O
sequence	B-Algorithm
alignment	I-Algorithm
of	O
protein	O
and	O
nucleotide	O
sequences	O
.	O
</s>
<s>
It	O
is	O
licensed	B-License
as	O
public	O
domain	O
.	O
</s>
<s>
The	O
method	O
was	O
published	O
by	O
Robert	B-Application
C	I-Application
.	I-Application
Edgar	I-Application
in	O
two	O
papers	O
in	O
2004	O
.	O
</s>
<s>
The	O
first	O
paper	O
,	O
published	O
in	O
Nucleic	O
Acids	O
Research	O
,	O
introduced	O
the	O
sequence	B-Algorithm
alignment	I-Algorithm
algorithm	O
.	O
</s>
<s>
UPGMA	B-Algorithm
clusters	O
the	O
distance	O
matrix	O
to	O
produce	O
a	O
binary	O
tree	O
.	O
</s>
<s>
This	O
continues	O
until	O
there	O
is	O
a	O
multiple	O
sequence	B-Algorithm
alignment	I-Algorithm
of	O
all	O
input	O
sequences	O
at	O
the	O
root	O
of	O
the	O
tree	O
.	O
</s>
<s>
This	O
stage	O
focuses	O
on	O
obtaining	O
a	O
more	O
optimal	O
tree	O
by	O
calculating	O
the	O
Kimura	O
distance	O
for	O
each	O
pair	O
of	O
input	O
sequences	O
using	O
the	O
multiple	O
sequence	B-Algorithm
alignment	I-Algorithm
obtained	O
in	O
Stage	O
one	O
,	O
and	O
creates	O
a	O
second	O
distance	O
matrix	O
.	O
</s>
<s>
UPGMA	B-Algorithm
clusters	O
this	O
distance	O
matrix	O
to	O
obtain	O
a	O
second	O
binary	O
tree	O
.	O
</s>
<s>
A	O
progressive	O
alignment	O
is	O
performed	O
to	O
obtain	O
a	O
multiple	O
sequence	B-Algorithm
alignment	I-Algorithm
like	O
in	O
Stage	O
1	O
,	O
but	O
it	O
is	O
optimized	O
by	O
only	O
computing	O
alignments	O
in	O
subtrees	O
whose	O
branching	O
orders	O
have	O
changed	O
from	O
the	O
first	O
binary	O
tree	O
,	O
resulting	O
in	O
a	O
more	O
accurate	O
alignment	O
.	O
</s>
<s>
A	O
new	O
multiple	O
sequence	B-Algorithm
alignment	I-Algorithm
is	O
produced	O
by	O
re-aligning	O
the	O
subtree	O
profiles	O
.	O
</s>
<s>
MUSCLE	O
is	O
often	O
used	O
as	O
a	O
replacement	O
for	O
Clustal	B-Application
,	O
since	O
it	O
usually	O
(	O
but	O
not	O
always	O
)	O
gives	O
better	O
sequence	B-Algorithm
alignments	I-Algorithm
,	O
depending	O
on	O
the	O
chosen	O
options	O
.	O
</s>
<s>
is	O
significantly	O
faster	O
than	O
Clustal	B-Application
,	O
more	O
so	O
for	O
larger	O
alignments	O
.	O
</s>
<s>
MUSCLE	O
is	O
integrated	O
into	O
DNASTAR	O
's	O
Lasergene	O
software	O
,	O
Geneious	O
,	O
and	O
MacVector	B-Application
and	O
is	O
available	O
in	O
Sequencher	O
,	O
MEGA	B-Application
,	O
and	O
UGENE	B-Language
as	O
a	O
plug-in	B-Application
.	O
</s>
