<s>
The	O
Phylogenetic	B-Application
Assignment	I-Application
of	I-Application
Named	I-Application
Global	I-Application
Outbreak	I-Application
Lineages	I-Application
(	O
PANGOLIN	B-Application
)	O
is	O
a	O
software	O
tool	O
developed	O
by	O
Dr.	O
Áine	O
O'Toole	O
and	O
members	O
of	O
the	O
Andrew	O
Rambaut	O
laboratory	O
,	O
with	O
an	O
associated	O
web	O
application	O
developed	O
by	O
the	O
Centre	O
for	O
Genomic	O
Pathogen	O
Surveillance	O
in	O
South	O
Cambridgeshire	O
.	O
</s>
<s>
A	O
user	O
with	O
a	O
full	O
genome	O
sequence	O
of	O
a	O
sample	O
of	O
SARS-CoV-2	O
can	O
use	O
the	O
tool	O
to	O
submit	O
that	O
sequence	O
,	O
which	O
is	O
then	O
compared	O
with	O
other	O
genome	O
sequences	O
,	O
and	O
assigned	O
the	O
most	O
likely	O
lineage	O
(	O
PANGO	B-Application
lineage	I-Application
)	O
.	O
</s>
<s>
It	O
is	O
named	O
after	O
the	O
pangolin	B-Application
.	O
</s>
<s>
PANGOLIN	B-Application
is	O
a	O
key	O
component	O
underpinning	O
the	O
PANGO	O
nomenclature	O
system	O
.	O
</s>
<s>
(	O
2020	O
)	O
,	O
a	O
PANGO	B-Application
Lineage	I-Application
is	O
described	O
as	O
a	O
cluster	O
of	O
sequences	O
that	O
are	O
associated	O
with	O
an	O
epidemiological	O
event	O
,	O
for	O
instance	O
an	O
introduction	O
of	O
the	O
virus	O
into	O
a	O
distinct	O
geographic	O
area	O
with	O
evidence	O
of	O
onward	O
spread	O
.	O
</s>
<s>
Both	O
the	O
tool	O
and	O
the	O
PANGOLIN	B-Application
nomenclature	O
system	O
have	O
been	O
used	O
extensively	O
during	O
the	O
COVID-19	O
pandemic	O
.	O
</s>
<s>
Distinct	O
from	O
the	O
PANGOLIN	B-Application
tool	O
,	O
Pango	B-Application
lineages	I-Application
are	O
regularly	O
,	O
manually	O
curated	O
based	O
on	O
the	O
current	O
globally	O
circulating	O
diversity	O
.	O
</s>
<s>
A	O
large	O
phylogenetic	O
tree	O
is	O
constructed	O
from	O
an	O
alignment	O
containing	O
publicly	O
available	O
SARS-CoV-2	O
genomes	O
,	O
and	O
sub-clusters	O
of	O
sequences	O
in	O
this	O
tree	O
are	O
manually	O
examined	O
and	O
cross-referenced	O
against	O
epidemiological	O
information	O
to	O
designate	O
new	O
lineages	O
;	O
these	O
can	O
be	O
designated	O
by	O
data	O
producers	O
,	O
and	O
lineage	O
suggestions	O
can	O
be	O
submitted	O
to	O
the	O
Pango	O
team	O
via	O
a	O
GitHub	B-Application
issue	O
request	O
.	O
</s>
<s>
The	O
current	O
version	O
of	O
pangoLEARN	O
uses	O
a	O
classification	O
tree	O
,	O
based	O
on	O
the	O
scikit-learn	B-Application
implementation	O
of	O
a	O
decision	O
tree	O
classifier	O
.	O
</s>
<s>
Originally	O
,	O
PANGOLIN	B-Application
used	O
a	O
maximum-likelihood-based	O
assignment	O
algorithm	O
to	O
assign	O
query	O
SARS-CoV-2	O
the	O
most	O
likely	O
lineage	O
sequence	O
.	O
</s>
<s>
PANGOLIN	B-Application
is	O
available	O
as	O
a	O
command-line-based	O
tool	O
,	O
downloadable	O
from	O
Conda	B-Application
and	O
from	O
a	O
GitHub	B-Application
repository	O
,	O
and	O
as	O
a	O
web-application	O
with	O
a	O
drag-and-drop	O
graphical	O
user	O
interface	O
.	O
</s>
<s>
The	O
PANGOLIN	B-Application
web	O
application	O
has	O
assigned	O
more	O
than	O
512,000	O
unique	O
SARS-CoV-2	O
sequences	O
as	O
of	O
January	O
2021	O
.	O
</s>
<s>
PANGOLIN	B-Application
was	O
created	O
by	O
Áine	O
O'Toole	O
and	O
the	O
Rambaut	O
lab	O
and	O
released	O
on	O
5	O
April	O
2020	O
.	O
</s>
<s>
The	O
main	O
developers	O
of	O
PANGOLIN	B-Application
are	O
Áine	O
O'Toole	O
and	O
Emily	O
Scher	O
;	O
many	O
others	O
have	O
contributed	O
to	O
various	O
aspects	O
of	O
the	O
tool	O
,	O
including	O
Ben	O
Jackson	O
,	O
J.T.	O
</s>
<s>
The	O
PANGOLIN	B-Application
web	O
application	O
was	O
developed	O
by	O
the	O
Centre	O
for	O
Genomic	O
Pathogen	O
Surveillance	O
,	O
namely	O
Anthony	O
Underwood	O
,	O
Ben	O
Taylor	O
,	O
Corin	O
Yeats	O
,	O
Khali	O
Abu-Dahab	O
,	O
and	O
David	O
Aanensen	O
.	O
</s>
