<s>
The	O
ViennaRNA	B-Application
Package	I-Application
is	O
a	O
set	O
of	O
standalone	O
programs	O
and	O
libraries	O
used	O
for	O
prediction	O
and	O
analysis	O
of	O
RNA	O
secondary	O
structures	O
.	O
</s>
<s>
The	O
source	O
code	O
for	O
the	O
package	O
is	O
distributed	O
freely	B-Application
and	O
compiled	O
binaries	O
are	O
available	O
for	O
Linux	B-Application
,	O
macOS	B-Application
and	O
Windows	O
platforms	O
.	O
</s>
<s>
Secondary	O
structure	O
prediction	O
is	O
commonly	O
done	O
using	O
approaches	O
like	O
dynamic	B-Algorithm
programming	I-Algorithm
,	O
energy	O
minimisation	O
(	O
for	O
most	O
stable	O
structure	O
)	O
and	O
generating	O
suboptimal	O
structures	O
.	O
</s>
<s>
A	O
large	O
number	O
of	O
structure	B-Application
prediction	I-Application
tools	I-Application
have	O
been	O
implemented	O
as	O
well	O
.	O
</s>
<s>
The	O
first	O
version	O
of	O
the	O
ViennaRNA	B-Application
Package	I-Application
was	O
published	O
by	O
Hofacker	O
et	O
al	O
.	O
</s>
<s>
The	O
package	O
distributed	O
tools	O
to	O
compute	O
either	O
minimum	O
free	O
energy	O
structures	O
or	O
partition	O
functions	O
of	O
RNA	O
molecules	O
;	O
both	O
using	O
the	O
idea	O
of	O
dynamic	B-Algorithm
programming	I-Algorithm
.	O
</s>
<s>
Additionally	O
,	O
the	O
package	O
also	O
contained	O
a	O
statistics	O
suite	O
with	O
routines	O
for	O
cluster	B-Algorithm
analysis	I-Algorithm
,	O
statistical	O
geometry	O
,	O
and	O
split	O
decomposition	O
.	O
</s>
<s>
A	O
number	O
of	O
major	O
systemic	O
changes	O
were	O
introduced	O
in	O
this	O
version	O
with	O
the	O
use	O
of	O
a	O
new	O
parametrized	O
energy	O
model	O
(	O
Turner	O
2004	O
)	O
,	O
restructuring	O
of	O
the	O
RNAlib	O
to	O
support	O
concurrent	O
computations	O
in	O
thread-safe	O
manner	O
,	O
improvements	O
to	O
the	O
API	B-Application
,	O
and	O
inclusion	O
of	O
several	O
new	O
auxiliary	O
tools	O
.	O
</s>
<s>
Furthermore	O
,	O
other	O
features	O
included	O
additional	O
output	O
information	O
such	O
as	O
centroid	O
structures	O
and	O
maximum	O
expected	O
accuracy	O
structures	O
derived	O
from	O
base	O
pairing	O
probabilities	O
,	O
or	O
z-scores	O
for	O
locally	O
stable	O
secondary	O
structures	O
,	O
and	O
support	O
for	O
input	O
in	O
FASTA	B-Application
format	O
.	O
</s>
<s>
The	O
tools	O
provided	O
by	O
the	O
ViennaRNA	B-Application
Package	I-Application
are	O
also	O
available	O
for	O
public	O
use	O
through	O
a	O
web	O
interface	O
.	O
</s>
<s>
In	O
addition	O
to	O
prediction	O
and	O
analysis	O
tools	O
,	O
the	O
ViennaRNA	B-Application
Package	I-Application
contains	O
several	O
scripts	O
and	O
utilities	O
for	O
plotting	O
and	O
input-output	O
processing	O
.	O
</s>
