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[
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[
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[
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GP
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n
o
f
t
h
e
p
r
o
g
r
a
m
f
o
r
p
ar
alleliza
tio
n
[
8
]
.
T
h
e
m
e
th
o
d
is
d
iv
id
ed
in
to
f
o
u
r
s
ta
g
e
s
th
at
ca
n
b
e
s
ee
n
i
n
Fi
g
u
r
e
1.
Fig
u
r
e
1
.
R
esear
ch
m
eth
o
d
2
.
1
.
I
dentif
ica
t
io
n
A
t
th
i
s
s
ta
g
e
w
e
id
en
ti
f
y
th
e
ca
lcu
latio
n
co
m
p
o
n
e
n
ts
th
at
ca
n
b
e
r
u
n
in
p
ar
allel
f
o
r
th
e
f
ir
s
t
a
n
d
s
ec
o
n
d
s
ta
g
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o
f
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h
e
p
r
o
g
r
es
s
iv
e
M
S
A
C
l
u
s
talW
alg
o
r
it
h
m
[
8
]
.
I
d
en
tif
icatio
n
is
d
o
n
e
b
y
e
x
a
m
in
in
g
t
h
e
p
s
eu
d
o
co
d
e
o
f
b
o
th
s
tag
e
s
o
f
th
e
al
g
o
r
ith
m
.
T
h
e
f
ir
s
t
s
tag
e
o
f
p
r
o
g
r
es
s
i
v
e
M
S
A
C
l
u
s
tal
W
is
co
m
p
u
ti
n
g
t
h
e
d
is
tan
ce
m
atr
i
x
u
s
in
g
p
air
w
i
s
e
alig
n
m
en
t.
I
n
th
is
r
e
s
ea
r
ch
,
th
e
d
y
n
a
m
ic
p
r
o
g
r
a
m
m
in
g
alg
o
r
ith
m
Nee
d
le
m
a
n
-
W
u
n
s
c
h
[
9
]
is
u
s
ed
as
t
h
e
o
p
ti
m
al
g
lo
b
al
alig
n
m
e
n
t
o
f
t
h
e
t
w
o
s
eq
u
e
n
ce
s
[
1
0
]
.
T
h
e
alg
o
r
ith
m
h
a
s
th
r
ee
s
tag
e
s
:
i
n
itia
lizatio
n
,
s
co
r
in
g
m
atr
i
x
ca
lc
u
latio
n
,
an
d
tr
ac
eb
ac
k
.
T
h
e
s
co
r
in
g
m
atr
ix
v
alu
e
i
s
o
b
tain
ed
b
y
f
i
n
d
in
g
th
e
m
ax
i
m
u
m
v
al
u
e
o
f
th
e
ce
ll
o
n
t
h
e
lef
t,
t
h
e
to
p
a
n
d
th
e
d
iag
o
n
al
o
f
t
h
e
in
ten
d
e
d
ce
ll.
T
h
e
d
is
tan
ce
v
alu
e
b
et
w
ee
n
th
ese
s
eq
u
en
ce
s
is
ca
lcu
lated
u
s
in
g
E
q
u
atio
n
1
.
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h
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d
is
tan
ce
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alu
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s
b
et
w
ee
n
th
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s
eq
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n
ce
s
ar
e
s
to
r
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in
th
e
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n
ce
m
atr
ix
.
(
1
)
T
h
e
s
ec
o
n
d
s
tag
e
is
m
ak
in
g
a
g
u
id
e
tr
ee
u
s
i
n
g
n
e
ig
h
b
o
r
-
j
o
in
in
g
al
g
o
r
ith
m
[
8
]
.
T
h
is
alg
o
r
ith
m
u
s
es
d
is
tan
ce
m
atr
i
x
D
f
r
o
m
p
ai
r
w
i
s
e
ali
g
n
m
e
n
t
a
s
t
h
e
in
p
u
t
v
al
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e,
w
h
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D
(
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i
s
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h
e
d
is
tan
ce
b
et
w
ee
n
s
eq
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en
ce
s
/
n
o
d
es
i
an
d
j
.
B
asi
ca
ll
y
,
th
i
s
alg
o
r
it
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m
s
e
lects
n
o
d
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iter
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u
n
ti
l le
a
v
in
g
a
s
in
g
le
n
o
d
e
[
1
2
]
.
P
air
s
i
an
d
j
a
r
e
s
elec
ted
b
y
m
i
n
i
m
izi
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g
Q
(
i,
j)
a
s
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n
E
q
u
atio
n
2
.
W
h
ile
th
e
v
al
u
e
o
f
u
(
l
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is
o
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tai
n
ed
ac
co
r
d
in
g
to
E
q
u
atio
n
3
.
(
2
)
(
3
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Evaluation Warning : The document was created with Spire.PDF for Python.
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9
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No
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1
,
J
an
u
ar
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201
8
:
234
–
2
42
236
No
tatio
n
r
is
th
e
n
u
m
b
er
o
f
r
e
m
ai
n
in
g
n
o
d
es.
T
h
e
m
a
tr
ix
w
il
l
b
e
u
p
d
ated
b
y
d
eletin
g
t
h
e
i
-
t
h
r
o
w
an
d
th
e
j
-
t
h
co
lu
m
n
w
h
en
th
e
m
i
n
i
m
u
m
Q(
i,j
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i
s
f
o
u
n
d
.
Ne
w
r
o
w
s
a
n
d
co
lu
m
n
s
ar
e
ad
d
ed
to
th
e
m
atr
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x
.
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h
e
d
is
tan
ce
b
et
w
ee
n
th
e
n
e
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n
o
d
e
a
an
d
th
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ai
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n
o
d
e
k
is
d
escr
ib
ed
in
E
q
u
atio
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4
.
(
4
)
2
.
2
.
Dec
o
m
po
s
it
io
n
A
t
t
h
is
s
ta
g
e,
t
h
e
id
e
n
ti
f
icatio
n
r
es
u
lt
s
ar
e
d
ec
o
m
p
o
s
ed
a
n
d
d
esig
n
ed
f
o
r
i
m
p
le
m
e
n
tatio
n
s
ce
n
ar
io
s
.
Dec
o
m
p
o
s
itio
n
o
f
p
ar
allel
co
m
p
o
n
en
t
s
is
d
o
n
e
b
y
a
n
al
y
zin
g
th
e
p
o
ten
t
ial
o
f
p
ar
allel
w
h
et
h
er
it
ca
n
b
e
d
ir
ec
tl
y
p
ar
alleled
o
r
r
eq
u
ir
e
s
p
ec
ial
tech
n
iq
u
e
s
.
Dec
o
m
p
o
s
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n
r
esu
lts
ar
e
u
s
ed
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elec
t
th
e
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r
o
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r
a
m
m
in
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m
o
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o
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esig
n
i
n
g
t
h
e
i
m
p
le
m
en
tatio
n
s
ce
n
ar
io
.
P
ar
allel
p
r
o
g
r
a
m
m
in
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m
o
d
el
u
s
ed
is
m
es
s
ag
e
p
as
s
in
g
,
s
h
ar
ed
m
e
m
o
r
y
a
n
d
h
y
b
r
id
.
I
n
m
e
s
s
a
g
e
p
ass
in
g
a
co
m
p
u
ta
tio
n
co
n
s
i
s
t
s
o
f
o
n
e
o
r
m
o
r
e
p
r
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ce
s
s
es
th
at
co
m
m
u
n
icate
w
it
h
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c
h
o
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h
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y
s
en
d
i
n
g
an
d
r
ec
eiv
in
g
m
es
s
ag
e
s
[
8
]
.
I
m
p
l
e
m
en
tatio
n
o
f
m
ess
a
g
e
p
as
s
i
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g
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o
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d
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s
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ted
m
e
m
o
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y
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m
u
s
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g
Me
s
s
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g
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P
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g
I
n
ter
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ac
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(
MP
I
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.
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o
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all
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ar
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a
m
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m
e
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s
e
it
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o
n
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n
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ter
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m
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le
m
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Op
e
n
M
u
lti
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s
s
in
g
(
Op
en
MP
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.
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y
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o
d
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l
co
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n
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t
h
e
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s
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an
d
s
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m
e
m
o
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y
.
2
.
3
.
I
m
ple
m
ent
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t
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n
T
h
e
r
esu
lt
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f
s
eq
u
e
n
tial
p
air
wis
e
ali
g
n
m
e
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g
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r
ith
m
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s
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u
s
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n
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MB
OSS
Nee
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B
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A
li
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n
m
e
n
t
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ST
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r
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m
NC
B
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th
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m
u
s
e
Nee
d
le
m
a
n
-
W
u
n
s
c
h
alg
o
r
it
h
m
.
Ver
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n
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o
n
e
t
w
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s
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DN
A
s
eq
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e
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.
T
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s
t
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er
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u
s
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A
n
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n
d
r
io
n
(
NC
_
0
0
3
4
1
5
.
1
)
an
d
N
ec
a
to
r
a
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n
u
s
mito
ch
o
n
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(
NC
_
0
0
3
4
1
6
.
2
)
.
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h
e
s
ec
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n
d
v
er
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ica
tio
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u
s
e
s
Hu
ma
n
P
a
p
illo
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s
typ
e
1
3
2
(
NC
_
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9
5
5
.
1
)
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d
Hu
ma
n
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lo
ma
viru
s
typ
e
1
3
4
(
NC
_
0
1
4
9
5
6
.
1
)
.
T
h
e
m
etr
ic
u
s
ed
to
co
m
p
ar
e
th
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s
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o
r
ith
m
is
a
s
i
m
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lar
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y
.
T
h
e
s
i
m
ilar
it
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s
th
e
p
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ce
n
tag
e
o
f
th
e
n
u
m
b
er
o
f
m
atc
h
i
n
g
c
h
ar
a
ct
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s
co
m
p
ar
ed
to
th
e
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g
t
h
o
f
th
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al
ig
n
m
en
t f
o
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m
ed
.
T
h
e
r
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lt
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t
h
e
n
ei
g
h
b
o
r
-
j
o
in
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r
ith
m
is
v
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if
ied
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s
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NJ
s
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t
w
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A
M
C
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ad
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s
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DDB
J
J
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.
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lu
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Dr
a
w
T
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ee
f
r
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P
h
y
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g
e
n
y
.
f
r
Fra
n
ce
.
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o
th
o
f
th
e
m
u
s
e
n
ei
g
h
b
o
r
-
j
o
in
in
g
al
g
o
r
ith
m
.
T
h
is
Ver
i
f
icatio
n
u
s
es
th
e
s
a
m
e
o
f
d
ata
s
eq
u
en
ce
s
i
n
p
air
w
i
s
e
ali
g
n
m
en
t
v
er
if
icatio
n
.
Ver
i
f
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io
n
is
d
o
n
e
u
s
i
n
g
v
is
u
aliza
t
io
n
d
ata
f
r
o
m
n
ei
g
h
b
o
r
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in
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o
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w
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u
tp
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t.
A
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s
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tag
e,
t
h
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n
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m
p
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m
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ted
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th
e
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t
er
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s
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te
s
ti
n
g
en
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n
m
e
n
t.
I
n
ea
ch
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ce
n
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io
,
b
o
th
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it
h
m
s
ar
e
r
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s
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n
g
a
v
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n
o
f
4
p
r
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ce
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s
,
8
p
r
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s
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r
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ce
s
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r
s
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As
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h
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t
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ated
DN
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e
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with
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p
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ce
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n
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p
iece
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o
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s
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u
e
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ce
s
.
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n
g
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s
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m
u
c
h
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1
0
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s
s
o
r
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ith
i
n
ea
ch
n
o
d
e,
s
o
th
at
r
eq
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ir
ed
in
ter
-
n
o
d
e
co
m
m
u
n
ica
tio
n
.
T
h
e
p
u
r
eOp
en
MP
s
ce
n
ar
io
d
iv
id
es
th
e
o
u
ter
lo
o
p
tas
k
in
t
h
e
clu
s
talW
-
p
air
w
i
s
e
A
li
g
n
m
e
n
t
(
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f
u
n
ctio
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u
s
i
n
g
Op
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MP
s
o
th
at
ea
c
h
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li
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f
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m
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x
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ted
p
ar
allel
b
y
th
e
th
r
ea
d
s
w
i
th
i
n
a
n
o
d
e.
Par
titi
o
n
d
ata
is
d
o
n
e
b
y
d
iv
id
in
g
t
h
e
n
u
m
b
er
o
f
s
eq
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e
n
ce
s
b
y
t
h
e
n
u
m
b
er
o
f
th
r
ea
d
s
u
s
ed
.
T
h
e
o
m
p
I
n
n
er
s
ce
n
ar
io
p
a
r
allels
d
ir
ec
tl
y
o
n
t
h
e
p
air
w
i
s
e
A
li
g
n
m
en
t(
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f
u
n
ctio
n
u
s
i
n
g
t
h
e
s
h
ar
ed
m
e
m
o
r
y
p
r
o
g
r
a
m
m
i
n
g
m
o
d
e
l.
T
h
e
r
is
k
o
f
d
ata
d
ep
en
d
en
c
y
is
ad
d
r
ess
ed
b
y
s
y
n
ch
r
o
n
izin
g
[
7
]
.
T
h
e
s
y
n
ch
r
o
n
izatio
n
i
s
d
o
n
e
in
t
h
e
f
o
r
m
o
f
ch
ec
k
i
n
g
th
e
ce
ll
s
r
eq
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ir
ed
in
th
e
ca
lc
u
latio
n
.
I
f
th
e
r
eq
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ir
ed
ce
ll
v
alu
e
is
av
ai
lab
le,
th
e
n
th
e
th
r
ea
d
ca
n
co
n
ti
n
u
e
its
w
o
r
k
.
B
u
t i
f
t
h
e
r
eq
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ir
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ce
ll is
n
o
t a
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ailab
le,
t
h
en
t
h
e
t
h
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w
ill
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h
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ca
u
s
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s
th
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s
ce
n
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io
to
b
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th
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p
r
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t
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ce
n
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h
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ar
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task
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W
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f
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i
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to
t
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p
r
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ce
s
s
o
r
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i
n
g
MP
I
,
th
e
n
ea
ch
p
r
o
ce
s
s
o
r
p
er
f
o
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m
s
th
e
p
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w
is
e
Alig
n
m
e
n
t(
)
f
u
n
ct
io
n
th
at
h
a
s
b
ee
n
p
ar
alleled
u
s
i
n
g
Op
e
n
MP
as
th
e
o
m
p
I
n
n
er
s
ce
n
ar
io
.
T
h
e
last
s
ce
n
ar
io
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m
p
i
O
m
p
Ou
ter
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I
t
is
a
h
y
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id
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ar
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p
o
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clu
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p
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is
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Alig
n
m
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n
t(
)
f
u
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n
.
T
h
is
s
ce
n
ar
io
d
iv
i
d
es
th
e
n
u
m
b
er
o
f
s
eq
u
e
n
ce
s
b
y
t
h
e
n
u
m
b
er
o
f
p
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s
s
o
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an
d
d
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ib
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tes
th
e
m
to
t
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co
m
p
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te
n
o
d
e
u
s
i
n
g
MP
I
.
T
h
e
r
esu
lti
n
g
p
ar
tit
io
n
d
at
a
is
f
u
r
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P
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f P
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A
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men
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N
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A
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m…
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A
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id
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239
s
u
b
d
iv
id
ed
b
y
Op
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MP
i
n
to
m
u
ltip
le
t
h
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s
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T
h
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en
d
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MP
I
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3
.
2
.
2
.
Neig
hb
o
r
-
J
o
ini
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T
h
e
id
en
tif
ica
tio
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s
u
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a
n
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e
in
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B
o
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ca
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e
h
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d
led
w
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th
a
p
ar
all
el
r
ed
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th
a
t
d
iv
id
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p
ar
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p
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ce
s
s
i
n
g
in
to
s
ev
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al
s
tep
s
r
es
u
lti
n
g
i
n
a
g
l
o
b
al
s
o
lu
tio
n
.
I
m
p
le
m
e
n
tatio
n
o
f
p
ar
allel
r
e
d
u
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n
ca
n
b
e
d
o
n
e
u
s
i
n
g
Op
e
n
MP
o
n
th
e
s
h
ar
ed
m
e
m
o
r
y
s
y
s
te
m
.
T
h
e
s
elec
tio
n
o
f
Op
e
n
MP
as
a
n
eig
h
b
o
r
-
j
o
in
in
g
al
g
o
r
ith
m
i
m
p
le
m
en
ta
tio
n
i
s
b
ased
o
n
t
w
o
t
h
i
n
g
s
.
First,
t
h
e
p
ar
allel
r
ed
u
ctio
n
is
m
o
r
e
s
u
itab
le
f
o
r
s
h
ar
ed
m
e
m
o
r
y
s
y
s
te
m
s
,
an
d
Op
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MP
h
as
a
p
ar
allel
r
ed
u
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n
f
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tu
r
e
th
at
is
ea
s
y
to
i
m
p
le
m
e
n
t
co
m
p
ar
ed
to
MP
I
.
Seco
n
d
,
t
h
e
s
tr
u
c
tu
r
e
o
f
t
h
e
n
eig
h
b
o
r
-
j
o
in
in
g
al
g
o
r
ith
m
c
o
n
s
is
ts
o
f
m
a
n
y
lo
o
p
co
n
s
tr
u
cts
w
h
ic
h
ar
e
th
e
co
m
p
u
ta
tio
n
al
lo
ad
o
f
a
n
alg
o
r
ith
m
.
Op
e
n
MP
is
d
esi
g
n
e
d
to
p
ar
allelize
lo
o
p
co
n
s
tr
u
cti
o
n
w
it
h
o
u
t
t
h
i
n
k
i
n
g
ab
o
u
t
co
m
m
u
n
icatio
n
i
s
s
u
e
s
as M
P
I
.
3
.
3
.
I
m
ple
m
ent
a
t
io
n
3
.
3
.
1
P
a
ir
w
i
s
e
Alig
n
m
ent
C
o
m
p
ar
is
o
n
o
f
s
i
m
i
lar
it
y
v
alu
es
o
n
th
e
s
eq
u
en
tial
p
air
w
i
s
e
alig
n
m
en
t
w
i
th
b
o
th
v
er
if
icatio
n
s
o
f
t
w
ar
e
ca
n
b
e
s
ee
n
i
n
T
ab
le
2
.
Si
m
ilar
it
y
o
f
p
air
w
i
s
e
alig
n
m
en
t
o
b
tain
ed
f
r
o
m
b
o
th
v
er
i
f
icatio
n
is
n
o
t
m
u
c
h
d
if
f
er
e
n
t
f
r
o
m
E
MB
O
SS
Nee
d
le
[
1
4
]
an
d
Glo
b
al
A
l
ig
n
m
e
n
t
B
L
A
ST
[
1
5
]
.
I
t
s
h
o
w
s
t
h
e
s
eq
u
en
tial
p
air
w
i
s
e
alig
n
m
e
n
t a
l
g
o
r
ith
m
i
n
th
is
s
t
u
d
y
h
as
s
u
cc
e
s
s
f
u
ll
y
v
er
i
f
ied
w
ith
o
th
er
s
o
f
t
w
ar
e.
T
ab
le
2
.
C
o
m
p
ar
is
o
n
o
f
Si
m
il
ar
it
y
Val
u
es
V
e
r
i
f
i
c
a
t
i
o
n
n
u
m
b
e
r
P
a
i
r
w
i
se
A
l
i
g
n
me
n
t
EM
B
O
S
S
N
e
e
d
l
e
G
l
o
b
a
l
A
l
i
g
n
me
n
t
B
L
A
S
T
1
8
3
.
7
%
8
3
.
1
%
8
2
.
7
%
2
6
2
.
9
%
5
6
.
8
%
5
9
.
8
%
I
m
p
le
m
e
n
tatio
n
o
f
t
h
e
f
iv
e
s
c
en
ar
io
s
is
d
o
n
e
o
n
4
,
8
an
d
2
0
p
r
o
ce
s
s
o
r
s
.
E
ac
h
s
ce
n
ar
io
h
as
d
if
f
er
en
t
co
n
f
i
g
u
r
atio
n
s
to
u
s
e
t
h
ese
t
h
r
ee
v
ar
iatio
n
s
.
T
h
e
p
u
r
eM
P
I
s
ce
n
ar
io
u
s
i
n
g
2
n
o
d
es
×
2
p
r
o
c
ess
o
r
s
,
2
n
o
d
es
×
4
p
r
o
ce
s
s
o
r
s
an
d
2
n
o
d
es
×
1
0
p
r
o
ce
s
s
o
r
s
f
o
r
co
n
f
i
g
u
r
atio
n
.
T
h
e
p
u
r
eOp
en
MP
an
d
o
m
p
I
n
n
er
s
ce
n
ar
io
s
u
s
e
4
th
r
ea
d
s
o
n
4
co
r
es
n
o
d
e
an
d
eig
h
t
t
h
r
ea
d
s
o
n
8
co
r
es
n
o
d
e,
2
0
th
r
ea
d
s
o
n
2
0
co
r
es
n
o
d
e.
T
h
e
m
p
i
O
m
p
I
n
n
e
r
an
d
m
p
i
O
m
p
O
u
ter
s
ce
n
ar
io
s
u
s
e
2
n
o
d
es ×
1
p
r
o
ce
s
s
o
r
×
2
t
h
r
ea
d
s
,
2
n
o
d
es ×
2
p
r
o
ce
s
s
o
r
s
×
2
th
r
ea
d
s
an
d
2
n
o
d
es ×
5
p
r
o
ce
s
s
o
r
s
×
2
th
r
ea
d
s
f
o
r
co
n
f
i
g
u
r
atio
n
.
3
.
3
.
2
.
Neig
hb
o
r
-
J
o
ini
ng
I
n
th
i
s
v
er
if
icat
io
n
o
f
n
ei
g
h
b
o
r
-
j
o
in
in
g
,
A
n
cy
lo
s
to
ma
d
u
o
d
en
a
le
mito
c
h
o
n
d
r
io
n
(
NC
_
0
0
3
4
1
5
.
1
)
is
s
y
m
b
o
lized
as
s
eq
1
,
N
ec
a
to
r
a
merica
n
u
s
mito
ch
o
n
d
r
io
n
(
NC
_
0
0
3
4
1
6
.
2
)
is
s
y
m
b
o
lize
d
as
s
eq
2
,
Hu
ma
n
p
a
p
illo
ma
viru
s
typ
e
1
3
2
(
N
C
_
0
1
4
9
5
5
.
1
)
is
s
y
m
b
o
lized
as
s
eq
3
an
d
Hu
ma
n
p
a
p
illo
ma
viru
s
typ
e
1
3
4
(
NC
_
0
1
4
9
5
6
.
1
)
is
s
y
m
b
o
lized
as
s
eq
4
.
Vis
u
aliza
tio
n
tr
ee
f
r
o
m
th
e
ca
lcu
la
tio
n
o
f
n
e
ig
h
b
o
r
-
j
o
in
in
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co
m
b
in
ed
alg
o
r
ith
m
p
r
o
v
ed
r
o
b
u
s
t in
t
h
e
v
ar
iatio
n
o
f
D
N
A
s
eq
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e
n
ce
s
.
Evaluation Warning : The document was created with Spire.PDF for Python.
I
SS
N
:
2
5
0
2
-
4752
I
n
d
o
n
esia
n
J
E
lec
E
n
g
&
C
o
m
p
Sci,
Vo
l
.
9
,
No
.
1
,
J
an
u
ar
y
201
8
:
234
–
2
42
242
ACK
NO
WL
E
D
G
M
E
NT
T
h
e
au
th
o
r
s
w
o
u
ld
lik
e
to
th
a
n
k
t
h
e
Ag
e
n
c
y
f
o
r
A
s
s
es
s
m
en
t
an
d
A
p
p
licatio
n
o
f
T
ec
h
n
o
lo
g
y
(
B
P
PT
)
f
o
r
th
e
s
c
h
o
lar
s
h
ip
f
u
n
d
an
d
t
h
e
g
r
id
co
m
p
u
ti
n
g
f
ac
ili
t
y
.
RE
F
E
R
E
NC
E
S
[1
]
M
a
c
e
d
o
EA
,
Bo
u
k
e
rc
h
e
A
.
Hy
b
rid
M
PI/
Op
e
n
M
P
stra
teg
y
fo
r
b
io
lo
g
ica
l
mu
l
ti
p
le
se
q
u
e
n
c
e
a
li
g
n
me
n
t
wit
h
DIAL
IGN
-
T
X
in
h
e
ter
o
g
e
n
e
o
u
s
mu
lt
ico
re
c
lu
ste
rs
.
IEE
E
In
t
e
rn
a
ti
o
n
a
l
P
a
ra
ll
e
l
&
Distrib
u
ted
P
r
o
c
e
ss
in
g
S
y
m
p
o
siu
m
.
S
h
a
n
g
h
a
i
.
2
0
1
1
:
4
1
8
-
4
2
5
.
[2
]
T
h
o
m
p
so
n
JD
,
Hig
g
in
s
D
G
,
G
ib
so
n
T
J.
CL
US
TAL
W
:
i
m
p
ro
v
in
g
th
e
se
n
siti
v
it
y
o
f
p
ro
g
re
ss
iv
e
m
u
lt
ip
le
se
q
u
e
n
c
e
a
li
g
n
m
e
n
t
th
ro
u
g
h
se
q
u
e
n
c
e
we
ig
h
ti
n
g
,
p
o
siti
o
n
-
sp
e
c
if
ic
g
a
p
p
e
n
a
l
ti
e
s
a
n
d
we
ig
h
t
m
a
tri
x
c
h
o
ice
.
Nu
c
leic
Acid
s
Res
.
1
9
9
4
;
2
2
(
2
2
)
:
4
6
7
3
-
4
6
8
0
.
[3
]
L
i
KB.
Clu
sta
lW
-
M
P
I:
Cl
u
sta
lW
a
n
a
ly
sis
u
sin
g
p
a
ra
ll
e
l
a
n
d
d
istri
b
u
ted
c
o
m
p
u
ti
n
g
.
Bi
o
i
n
fo
rm
a
ti
c
s
.
2
0
0
3
;
1
9
:
1
5
8
5
–
1
5
8
6
.
[4
]
S
a
tra
R,
Ku
s
u
m
a
WA
,
S
u
k
o
c
o
H.
Ac
c
e
ler
a
ti
n
g
c
o
m
p
u
tatio
n
o
f
DN
A
m
u
lt
ip
le
se
q
u
e
n
c
e
a
li
g
n
m
e
n
t
in
d
istr
ib
u
ted
e
n
v
iro
n
m
e
n
t.
T
e
lko
mn
ika
In
d
o
n
e
sia
n
J
o
u
rn
a
l
o
f
E
lec
trica
l
En
g
i
n
e
e
rin
g
.
2
0
1
4
;
1
2
(1
2
):
8
2
7
8
–
8
2
8
5
.
[5
]
L
iu
Y,
S
c
h
m
id
t
B,
Do
u
g
las
L
M
.
Pa
r
a
ll
e
l
re
c
o
n
str
u
c
ti
o
n
o
f
n
e
ig
h
b
o
r
-
jo
in
i
n
g
tre
e
s
fo
r
la
r
g
e
mu
lt
ip
le
se
q
u
e
n
c
e
a
li
g
n
me
n
ts
u
si
n
g
CUD
A.
P
r
o
c
e
e
d
in
g
s
o
f
2
3
r
d
IEE
E
In
ter
n
a
ti
o
n
a
l
P
a
ra
ll
e
l
&
Distrib
u
ted
P
r
o
c
e
ss
in
g
S
y
m
p
o
siu
m
.
Ro
m
e
.
2
0
0
9
.
[6
]
Zh
e
n
g
R,
Zh
a
n
g
Q,
Jin
H,
S
h
a
o
Z,
F
e
n
g
X
.
A
G
P
U
-
b
a
se
d
p
a
r
a
ll
e
l
m
e
th
o
d
f
o
r
e
v
o
lu
ti
o
n
a
ry
tree
c
o
n
str
u
c
ti
o
n
.
Co
mp
u
ter
s
a
n
d
El
e
c
trica
l
E
n
g
in
e
e
rin
g
.
2
0
1
4
;
4
0
(5
):
1
5
8
0
–
1
5
9
1
.
[7
]
Ak
b
a
r
A
R,
S
u
k
o
c
o
H,
Ku
su
m
a
WA
.
Co
m
p
a
riso
n
o
f
d
a
ta
p
a
rti
ti
o
n
i
n
g
sc
h
e
m
a
o
f
p
a
ra
ll
e
l
p
a
ir
w
i
se
a
li
g
n
m
e
n
t
o
n
sh
a
re
d
m
e
m
o
r
y
s
y
ste
m
.
T
e
lko
mn
ika
In
d
o
n
e
si
a
n
J
o
u
rn
a
l
o
f
E
lec
trica
l
E
n
g
i
n
e
e
rin
g
.
2
0
1
5
;
1
3
(
2
):
6
9
4
-
7
0
2
.
[8
]
Do
n
g
a
rra
J,
F
o
ste
r
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F
o
x
G
,
G
ro
p
p
W
,
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n
n
e
d
y
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T
o
rc
z
o
n
L
,
W
h
it
e
A
.
S
o
u
rc
e
Bo
o
k
o
f
P
a
ra
ll
e
l
Co
m
p
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ti
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g
.
S
a
n
F
ra
n
c
isc
o
:
M
o
rg
a
n
Ka
u
fm
a
n
n
P
u
b
li
sh
e
rs.
2
0
0
3
.
[9
]
Ne
e
d
le
m
a
n
S
B,
W
u
n
sc
h
CD.
A
g
e
n
e
ra
l
m
e
th
o
d
a
p
p
li
c
a
b
le
to
se
a
rc
h
f
o
r
si
m
il
a
rit
ies
in
t
h
e
a
m
in
o
a
c
id
se
q
u
e
n
c
e
o
f
tw
o
p
ro
tein
s.
J
o
u
r
n
a
l
o
f
M
o
lec
u
la
r B
io
l
o
g
y
.
1
9
7
0
;
4
8
:
4
4
3
-
4
5
3
.
[1
0
]
Uto
m
o
AW
,
Ku
su
m
a
WA
.
Pen
ja
ja
ra
n
g
lo
b
a
l
se
k
u
e
n
DNA
me
n
g
g
u
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k
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o
ritme
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e
d
lem
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n
–
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n
sc
h
.
S
e
m
in
a
r
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sio
n
a
l
d
a
n
Ra
p
a
t
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a
h
u
n
a
n
Bid
a
n
g
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I
P
A
(S
e
m
irata
2
0
1
4
)
.
Bo
g
o
r.
2
0
1
4
;
Bo
o
k
3
:
2
1
0
-
2
1
8
.
[1
1
]
S
a
it
o
u
N,
Ne
i
M
.
T
h
e
n
e
ig
h
b
o
r
-
jo
in
i
n
g
m
e
th
o
d
:
a
n
e
w
m
e
th
o
d
f
o
r
re
c
o
n
str
u
c
ti
n
g
p
h
y
lo
g
e
n
e
ti
c
tr
e
e
s.
M
o
lec
u
la
r
Bi
o
lo
g
y
a
n
d
Evo
l
u
ti
o
n
.
1
9
8
7
;
4
(4
):
4
0
6
-
4
2
5
.
[1
2
]
S
im
o
n
se
n
M
,
M
a
il
u
n
d
T
,
P
e
d
e
rs
e
n
CN.
R
a
p
id
Ne
i
g
h
b
o
u
r
J
o
i
n
i
n
g
.
P
ro
c
e
e
d
in
g
s
o
f
8
th
in
t
e
r
n
a
ti
o
n
a
l
w
o
rk
sh
o
p
o
n
a
lg
o
rit
h
m
s in
b
io
in
f
o
rm
a
ti
c
s.
Be
rl
in
.
2
0
0
8
.
Evaluation Warning : The document was created with Spire.PDF for Python.