<s>
The	O
Biopython	B-Library
project	O
is	O
an	O
open-source	B-Application
collection	O
of	O
non-commercial	O
Python	B-Language
tools	O
for	O
computational	O
biology	O
and	O
bioinformatics	O
,	O
created	O
by	O
an	O
international	O
association	O
of	O
developers	O
.	O
</s>
<s>
Separate	O
modules	O
extend	O
Biopython	B-Library
's	O
capabilities	O
to	O
sequence	B-Algorithm
alignment	I-Algorithm
,	O
protein	O
structure	O
,	O
population	O
genetics	O
,	O
phylogenetics	O
,	O
sequence	O
motifs	O
,	O
and	O
machine	O
learning	O
.	O
</s>
<s>
Biopython	B-Library
is	O
one	O
of	O
a	O
number	O
of	O
Bio*	O
projects	O
designed	O
to	O
reduce	O
code	O
duplication	O
in	O
computational	O
biology	O
.	O
</s>
<s>
Biopython	B-Library
development	O
began	O
in	O
1999	O
and	O
it	O
was	O
first	O
released	O
in	O
July	O
2000	O
.	O
</s>
<s>
It	O
was	O
developed	O
during	O
a	O
similar	O
time	O
frame	O
and	O
with	O
analogous	O
goals	O
to	O
other	O
projects	O
that	O
added	O
bioinformatics	O
capabilities	O
to	O
their	O
respective	O
programming	O
languages	O
,	O
including	O
BioPerl	B-Application
,	O
BioRuby	B-Application
and	O
BioJava	B-Language
.	O
</s>
<s>
In	O
2007	O
,	O
a	O
similar	O
Python	B-Language
project	O
,	O
namely	O
PyCogent	O
,	O
was	O
established	O
.	O
</s>
<s>
The	O
initial	O
scope	O
of	O
Biopython	B-Library
involved	O
accessing	O
,	O
indexing	O
and	O
processing	O
biological	O
sequence	O
files	O
.	O
</s>
<s>
As	O
of	O
version	O
1.77	O
,	O
Biopython	B-Library
no	O
longer	O
supports	O
Python	B-Language
2	O
.	O
</s>
<s>
Wherever	O
possible	O
,	O
Biopython	B-Library
follows	O
the	O
conventions	O
used	O
by	O
the	O
Python	B-Language
programming	I-Language
language	I-Language
to	O
make	O
it	O
easier	O
for	O
users	O
familiar	O
with	O
Python	B-Language
.	O
</s>
<s>
For	O
example	O
,	O
Seq	O
and	O
SeqRecord	O
objects	O
can	O
be	O
manipulated	O
via	O
slicing	O
,	O
in	O
a	O
manner	O
similar	O
to	O
Python	B-Language
's	O
strings	O
and	O
lists	O
.	O
</s>
<s>
It	O
is	O
also	O
designed	O
to	O
be	O
functionally	O
similar	O
to	O
other	O
Bio*	O
projects	O
,	O
such	O
as	O
BioPerl	B-Application
.	O
</s>
<s>
Biopython	B-Library
is	O
able	O
to	O
read	O
and	O
write	O
most	O
common	O
file	O
formats	O
for	O
each	O
of	O
its	O
functional	O
areas	O
,	O
and	O
its	O
license	O
is	O
permissive	O
and	O
compatible	O
with	O
most	O
other	O
software	O
licenses	O
,	O
which	O
allow	O
Biopython	B-Library
to	O
be	O
used	O
in	O
a	O
variety	O
of	O
software	O
projects	O
.	O
</s>
<s>
A	O
core	O
concept	O
in	O
Biopython	B-Library
is	O
the	O
biological	O
sequence	O
,	O
and	O
this	O
is	O
represented	O
by	O
the	O
Seq	O
class	O
.	O
</s>
<s>
A	O
Biopython	B-Library
Seq	O
object	O
is	O
similar	O
to	O
a	O
Python	B-Language
string	O
in	O
many	O
respects	O
:	O
it	O
supports	O
the	O
Python	B-Language
slice	O
notation	O
,	O
can	O
be	O
concatenated	O
with	O
other	O
sequences	O
and	O
is	O
immutable	O
.	O
</s>
<s>
Biopython	B-Library
can	O
read	O
and	O
write	O
to	O
a	O
number	O
of	O
common	O
sequence	O
formats	O
,	O
including	O
FASTA	O
,	O
FASTQ	O
,	O
GenBank	O
,	O
Clustal	B-Application
,	O
PHYLIP	O
and	O
NEXUS	O
.	O
</s>
<s>
When	O
reading	O
files	O
,	O
descriptive	O
information	O
in	O
the	O
file	O
is	O
used	O
to	O
populate	O
the	O
members	O
of	O
Biopython	B-Library
classes	O
,	O
such	O
as	O
SeqRecord	O
.	O
</s>
<s>
Very	O
large	O
sequence	O
files	O
can	O
exceed	O
a	O
computer	O
's	O
memory	O
resources	O
,	O
so	O
Biopython	B-Library
provides	O
various	O
options	O
for	O
accessing	O
records	O
in	O
large	O
files	O
.	O
</s>
<s>
They	O
can	O
be	O
loaded	O
entirely	O
into	O
memory	O
in	O
Python	B-Language
data	O
structures	O
,	O
such	O
as	O
lists	O
or	O
dictionaries	B-Application
,	O
providing	O
fast	O
access	O
at	O
the	O
cost	O
of	O
memory	O
usage	O
.	O
</s>
<s>
Through	O
the	O
Bio.Entrez	O
module	O
,	O
users	O
of	O
Biopython	B-Library
can	O
download	O
biological	O
data	O
from	O
NCBI	O
databases	O
.	O
</s>
<s>
A	O
variety	O
of	O
file	O
formats	O
are	O
supported	O
for	O
reading	O
and	O
writing	O
,	O
including	O
Newick	B-Data_Structure
,	O
NEXUS	O
and	O
phyloXML	O
.	O
</s>
<s>
Rooted	O
trees	O
can	O
be	O
drawn	O
in	O
ASCII	O
or	O
using	O
matplotlib	B-Language
(	O
see	O
Figure	O
1	O
)	O
,	O
and	O
the	O
Graphviz	B-Language
library	O
can	O
be	O
used	O
to	O
create	O
unrooted	O
layouts	O
(	O
see	O
Figure	O
2	O
)	O
.	O
</s>
<s>
The	O
GenomeDiagram	O
module	O
provides	O
methods	O
of	O
visualising	O
sequences	O
within	O
Biopython	B-Library
.	O
</s>
<s>
Sequences	O
can	O
be	O
drawn	O
in	O
a	O
linear	O
or	O
circular	O
form	O
(	O
see	O
Figure	O
3	O
)	O
,	O
and	O
many	O
output	O
formats	O
are	O
supported	O
,	O
including	O
PDF	B-Application
and	O
PNG	O
.	O
</s>
<s>
The	O
Bio.PDB	O
module	O
can	O
load	O
molecular	O
structures	O
from	O
PDB	O
and	O
mmCIF	O
files	O
,	O
and	O
was	O
added	O
to	O
Biopython	B-Library
in	O
2003	O
.	O
</s>
<s>
The	O
Bio.PopGen	O
module	O
adds	O
support	O
to	O
Biopython	B-Library
for	O
Genepop	O
,	O
a	O
software	O
package	O
for	O
statistical	O
analysis	O
of	O
population	O
genetics	O
.	O
</s>
<s>
Many	O
of	O
Biopython	B-Library
's	O
modules	O
contain	O
command	O
line	O
wrappers	O
for	O
commonly	O
used	O
tools	O
,	O
allowing	O
these	O
tools	O
to	O
be	O
used	O
from	O
within	O
Biopython	B-Library
.	O
</s>
<s>
These	O
wrappers	O
include	O
BLAST	B-Application
,	O
Clustal	B-Application
,	O
PhyML	O
,	O
EMBOSS	B-Application
and	O
SAMtools	B-Application
.	O
</s>
