<s>
CodonCode	B-General_Concept
Aligner	I-General_Concept
is	O
a	O
commercial	O
application	O
for	O
DNA	O
sequence	O
assembly	O
,	O
sequence	B-Algorithm
alignment	I-Algorithm
,	O
and	O
editing	O
on	O
Mac	B-Operating_System
OS	I-Operating_System
X	I-Operating_System
and	O
Windows	B-Application
.	O
</s>
<s>
Features	O
include	O
chromatogram	O
editing	O
,	O
end	O
clipping	O
,	O
and	O
vector	O
trimming	O
,	O
sequence	O
assembly	O
and	O
contig	O
editing	O
,	O
aligning	O
cDNA	O
against	O
genomic	O
templates	O
,	O
sequence	B-Algorithm
alignment	I-Algorithm
and	O
editing	O
,	O
alignment	O
of	O
contigs	O
to	O
each	O
other	O
with	O
ClustalW	B-Application
,	O
MUSCLE	B-Application
,	O
or	O
built-in	O
algorithms	O
,	O
mutation	O
detection	O
,	O
including	O
detection	O
of	O
heterozygous	O
single-nucleotide	O
polymorphism	O
,	O
analysis	O
of	O
heterozygous	O
insertions	O
and	O
deletions	O
,	O
start	O
online	O
BLAST	B-Application
searches	O
,	O
restriction	O
analysis	O
(	O
find	O
and	O
view	O
restriction	O
cut	O
sites	O
)	O
,	O
trace	O
sharpening	O
,	O
and	O
support	O
for	O
Phred	O
,	O
Phrap	B-Application
,	O
ClustalW	B-Application
,	O
and	O
MUSCLE	B-Application
.	O
</s>
<s>
The	O
first	O
beta	O
version	O
of	O
CodonCode	B-General_Concept
Aligner	I-General_Concept
was	O
released	O
in	O
April	O
2003	O
,	O
followed	O
by	O
the	O
first	O
full	O
version	O
in	O
June	O
2003	O
.	O
</s>
<s>
In	O
April	O
2009	O
,	O
CodonCode	B-General_Concept
Aligner	I-General_Concept
had	O
been	O
cited	O
in	O
more	O
than	O
400	O
scientific	O
publications	O
.	O
</s>
