<s>
UGENE	B-Language
is	O
computer	O
software	O
for	O
bioinformatics	O
.	O
</s>
<s>
It	O
works	O
on	O
personal	B-Device
computer	I-Device
operating	O
systems	O
such	O
as	O
Windows	B-Application
,	O
macOS	B-Application
,	O
or	O
Linux	B-Application
.	O
</s>
<s>
It	O
is	O
released	O
as	O
free	B-License
and	I-License
open-source	I-License
software	I-License
,	O
under	O
a	O
GNU	B-License
General	I-License
Public	I-License
License	I-License
(	O
GPL	B-License
)	O
version	O
2	O
.	O
</s>
<s>
UGENE	B-Language
helps	O
biologists	O
to	O
analyze	O
various	O
biological	O
genetics	O
data	O
,	O
such	O
as	O
sequences	O
,	O
annotations	O
,	O
multiple	O
alignments	O
,	O
phylogenetic	O
trees	O
,	O
NGS	O
assemblies	O
,	O
and	O
others	O
.	O
</s>
<s>
The	O
data	O
can	O
be	O
stored	O
both	O
locally	O
(	O
on	O
a	O
personal	B-Device
computer	I-Device
)	O
and	O
on	O
a	O
shared	O
storage	O
(	O
e.g.	O
,	O
a	O
lab	O
database	O
)	O
.	O
</s>
<s>
UGENE	B-Language
integrates	O
dozens	O
of	O
well-known	O
biological	O
tools	O
,	O
algorithms	O
,	O
and	O
original	O
tools	O
in	O
the	O
context	O
of	O
genomics	O
,	O
evolutionary	O
biology	O
,	O
virology	O
,	O
and	O
other	O
branches	O
of	O
life	O
science	O
.	O
</s>
<s>
UGENE	B-Language
provides	O
a	O
graphical	B-Application
user	I-Application
interface	I-Application
(	O
GUI	B-Application
)	O
for	O
the	O
pre-built	O
tools	O
so	O
biologists	O
with	O
no	O
computer	B-General_Concept
programming	I-General_Concept
skills	O
can	O
access	O
those	O
tools	O
more	O
easily	O
.	O
</s>
<s>
Using	O
UGENE	B-Language
Workflow	B-Operating_System
Designer	O
,	O
it	O
is	O
possible	O
to	O
streamline	O
a	O
multi-step	O
analysis	O
.	O
</s>
<s>
The	O
workflow	B-Operating_System
consists	O
of	O
blocks	O
such	O
as	O
data	O
readers	O
,	O
blocks	O
executing	O
embedded	O
tools	O
and	O
algorithms	O
,	O
and	O
data	O
writers	O
.	O
</s>
<s>
Blocks	O
can	O
be	O
created	O
with	O
command	B-Application
line	I-Application
tools	I-Application
or	O
a	O
script	O
.	O
</s>
<s>
A	O
set	O
of	O
sample	O
workflows	B-Operating_System
is	O
available	O
in	O
the	O
Workflow	B-Operating_System
Designer	O
,	O
to	O
annotate	O
sequences	O
,	O
convert	O
data	O
formats	O
,	O
analyze	O
NGS	O
data	O
,	O
etc	O
.	O
</s>
<s>
Beside	O
the	O
graphical	B-Application
interface	I-Application
,	O
UGENE	B-Language
also	O
has	O
a	O
command-line	B-Application
interface	I-Application
.	O
</s>
<s>
Workflows	B-Operating_System
may	O
also	O
be	O
executed	O
thereby	O
.	O
</s>
<s>
To	O
improve	O
performance	O
,	O
UGENE	B-Language
uses	O
multi-core	B-Architecture
processors	I-Architecture
(	O
CPUs	O
)	O
and	O
graphics	B-Architecture
processing	I-Architecture
units	I-Architecture
(	O
GPUs	B-Architecture
)	O
to	O
optimize	O
a	O
few	O
algorithms	O
.	O
</s>
<s>
Before	O
browsing	O
assembly	O
data	O
in	O
UGENE	B-Language
,	O
an	O
input	O
file	O
is	O
converted	O
to	O
a	O
UGENE	B-Language
database	O
file	O
automatically	O
.	O
</s>
<s>
UGENE	B-Language
Workflow	B-Operating_System
Designer	O
allows	O
creating	O
and	O
running	O
complex	O
computational	O
workflow	B-Operating_System
schemas	O
.	O
</s>
<s>
The	O
distinguishing	O
feature	O
of	O
Workflow	B-Operating_System
Designer	O
,	O
relative	O
to	O
other	O
bioinformatics	B-Application
workflow	I-Application
management	I-Application
systems	I-Application
is	O
that	O
workflows	B-Operating_System
are	O
executed	O
on	O
a	O
local	O
computer	O
.	O
</s>
<s>
The	O
elements	O
that	O
a	O
workflow	B-Operating_System
consists	O
of	O
correspond	O
to	O
the	O
bulk	O
of	O
algorithms	O
integrated	O
into	O
UGENE	B-Language
.	O
</s>
<s>
Using	O
Workflow	B-Operating_System
Designer	O
also	O
allows	O
creating	O
custom	O
workflow	B-Operating_System
elements	O
.	O
</s>
<s>
The	O
elements	O
can	O
be	O
based	O
on	O
a	O
command-line	B-Application
tool	I-Application
or	O
a	O
script	O
.	O
</s>
<s>
Workflows	B-Operating_System
are	O
stored	O
in	O
a	O
special	O
text	O
format	O
.	O
</s>
<s>
A	O
workflow	B-Operating_System
can	O
be	O
run	O
using	O
the	O
graphical	B-Application
interface	I-Application
or	O
launched	O
from	O
the	O
command	B-Application
line	I-Application
.	O
</s>
<s>
The	O
graphical	B-Application
interface	I-Application
also	O
allows	O
controlling	O
the	O
workflow	B-Operating_System
execution	O
,	O
storing	O
the	O
parameters	O
,	O
and	O
so	O
on	O
.	O
</s>
<s>
There	O
is	O
an	O
embedded	O
library	O
of	O
workflow	B-Operating_System
samples	O
to	O
convert	O
,	O
filter	O
,	O
and	O
annotate	O
data	O
,	O
with	O
several	O
pipelines	O
to	O
analyze	O
NGS	O
data	O
developed	O
in	O
collaboration	O
with	O
NIH	O
NIAID	O
.	O
</s>
<s>
A	O
wizard	O
is	O
available	O
for	O
each	O
workflow	B-Operating_System
sample	O
.	O
</s>
<s>
UGENE	B-Language
is	O
primarily	O
developed	O
by	O
Unipro	O
LLC	O
with	O
headquarters	O
in	O
Akademgorodok	O
of	O
Novosibirsk	O
,	O
Russia	O
.	O
</s>
