<s>
This	O
is	O
a	O
list	O
of	O
computer	O
software	O
which	O
is	O
made	O
for	O
bioinformatics	O
and	O
released	O
under	O
open-source	B-Application
software	I-Application
licenses	O
with	O
articles	O
in	O
Wikipedia	O
.	O
</s>
<s>
Software	O
Description	O
Platform	O
License	O
Developer	O
.NET	B-Application
Bio	I-Application
Language-neutral	O
toolkit	O
built	O
using	O
the	O
Microsoft	O
4.0	O
.NET	B-Application
Framework	I-Application
to	O
help	O
developers	O
,	O
researchers	O
,	O
and	O
scientists	O
.NET	B-Application
Framework	I-Application
Apache	B-Application
Collaborative	O
project	O
AMPHORA	B-Application
Metagenomics	O
analysis	O
software	O
Linux	B-Application
GPL	B-License
Anduril	B-Application
Component-based	O
workflow	B-Operating_System
framework	O
for	O
data	O
analysis	O
Linux	B-Application
,	O
macOS	B-Application
,	O
Windows	B-Application
GPL	B-License
University	O
of	O
Helsinki	O
Ascalaph	B-Application
Designer	I-Application
Computer	O
program	O
for	O
general	O
purpose	O
molecular	O
modelling	O
for	O
molecular	O
design	O
and	O
simulations	O
.	O
</s>
<s>
GPLv2	O
Agile	O
Molecule	O
AutoDock	B-Application
Suite	O
of	O
automated	O
docking	O
tools	O
GPL	B-License
Avogadro	B-Language
C++	B-Language
(	O
Qt	O
)	O
based	O
molecule	O
editor	O
and	O
visualizer	O
for	O
in	O
computational	O
chemistry	O
,	O
molecular	O
modeling	O
,	O
bioinformatics	O
,	O
materials	O
science	O
,	O
and	O
related	O
areas	O
.	O
</s>
<s>
GPL	B-License
BEDtools	O
"	O
Genome	O
arithmetic	O
"	O
--	O
manipulation	O
of	O
coordinate	O
sets	O
and	O
the	O
extraction	O
of	O
sequences	O
from	O
a	O
BED	O
file	O
.	O
</s>
<s>
Linux	B-Application
MIT	B-License
QuinlanLab	O
,	O
University	O
of	O
Utah	O
Bioclipse	B-Language
Visual	O
platform	O
for	O
chemo	O
-	O
and	O
bioinformatics	O
based	O
on	O
the	O
Eclipse	B-Application
Rich	O
Client	O
Platform	O
(	O
RCP	O
)	O
Eclipse	B-License
Public	I-License
The	O
Bioclipse	B-Language
Project	O
Bioconductor	B-Application
R	B-Language
(	O
programming	O
language	O
)	O
language	O
toolkit	O
Linux	B-Application
,	O
macOS	B-Application
,	O
Windows	B-Application
Artistic	B-License
2.0	O
Fred	O
Hutchinson	O
Cancer	O
Research	O
Center	O
BioJava	B-Language
Java	B-Device
library	O
functions	O
for	O
manipulating	O
sequences	O
,	O
protein	O
structures	O
,	O
file	O
parsers	O
,	O
CORBA	O
interoperability	O
,	O
Distributed	O
Annotation	O
System	O
(	O
DAS	O
)	O
,	O
access	O
to	O
AceDB	O
,	O
dynamic	O
programming	O
,	O
and	O
simple	O
statistical	O
routines	O
Linux	B-Application
,	O
macOS	B-Application
,	O
Windows	B-Application
LGPL	B-Application
v2.1	O
Open	B-Application
Bioinformatics	I-Application
Foundation	I-Application
BioJS	B-Application
JavaScript	B-Language
library	O
of	O
components	O
to	O
visualize	O
biological	O
data	O
Web	B-Application
browser	I-Application
Apache	B-Application
BioMOBY	B-Language
Registry	O
of	O
web	O
services	O
Web	B-Application
browser	I-Application
Artistic	B-License
Open	B-Application
Bioinformatics	I-Application
Foundation	I-Application
BioPerl	B-Application
Perl	B-Language
language	I-Language
toolkit	O
Cross-platform	B-Operating_System
Artistic	B-License
,	O
GPL	B-License
Open	B-Application
Bioinformatics	I-Application
Foundation	I-Application
BioPHP	B-Application
PHP	B-Application
language	I-Application
toolkit	O
with	O
classes	O
for	O
DNA	O
and	O
protein	O
sequence	O
analysis	O
,	O
alignment	O
,	O
database	O
parsing	O
,	O
and	O
other	O
bioinformatics	O
tools	O
Cross-platform	B-Operating_System
GPL	B-License
v2	O
Open	B-Application
Bioinformatics	I-Application
Foundation	I-Application
Biopython	B-Library
Python	B-Language
language	I-Language
toolkit	O
Cross-platform	B-Operating_System
BiopythonBiopython	O
License	O
Open	B-Application
Bioinformatics	I-Application
Foundation	I-Application
BioRuby	B-Application
Ruby	B-Language
language	I-Language
toolkit	O
GPL	B-License
v2	O
or	O
Ruby	B-License
Open	B-Application
Bioinformatics	I-Application
Foundation	I-Application
BLAST	O
Algorithm	O
and	O
program	O
for	O
comparing	O
primary	O
biological	O
sequence	O
information	O
,	O
including	O
DNA	O
and	O
protein	O
sequences	O
.	O
</s>
<s>
Cross-platform	B-Operating_System
Public	O
domain	O
National	O
Center	O
for	O
Biotechnology	O
Information	O
CP2K	B-Application
Perform	O
atomistic	O
simulations	O
of	O
solid	O
state	O
,	O
liquid	O
,	O
molecular	O
and	O
biological	O
systems	O
,	O
written	O
in	O
Fortran	O
2003	O
.	O
</s>
<s>
GPL	B-License
and	O
LGPL	B-Application
Free	O
open	O
source	O
GNU	O
GPLv2	O
or	O
later	O
EMBOSS	B-Application
Suite	O
of	O
packages	O
for	O
sequencing	O
,	O
searching	O
,	O
etc	O
.	O
</s>
<s>
written	O
in	O
C	O
GPL	B-License
and	O
LGPL	B-Application
Collaborative	O
project	O
Galaxy	B-Application
Scientific	B-Application
workflow	I-Application
and	O
data	B-General_Concept
integration	I-General_Concept
system	O
Unix-like	B-Operating_System
Academic	B-License
Free	I-License
Collaborative	O
project	O
GenePattern	O
Scientific	B-Application
workflow	I-Application
system	I-Application
that	O
provides	O
access	O
to	O
hundreds	O
of	O
genomic	O
analysis	O
tools	O
Unix-like	B-Operating_System
(	O
public	O
server	O
)	O
;	O
Linux	B-Application
,	O
macOS	B-Application
,	O
Windows	B-Application
MIT	B-License
Broad	O
Institute	O
,	O
UC	O
San	O
Diego	O
Geworkbench	B-Algorithm
Genomic	O
data	B-General_Concept
integration	I-General_Concept
platform	O
Linux	B-Application
,	O
macOS	B-Application
,	O
Windows	B-Application
GeWorkbench	B-Algorithm
License	O
Columbia	O
University	O
GMOD	O
Toolkit	O
to	O
address	O
many	O
common	O
challenges	O
at	O
biological	O
databases	O
Unix-like	B-Operating_System
(	O
server	O
)	O
,	O
Web	B-Application
browser	I-Application
(	O
client	O
)	O
Varies	O
depending	O
on	O
tool	O
Collaborative	O
project	O
GenGIS	O
Application	O
that	O
allows	O
combining	O
digital	O
map	O
data	O
with	O
information	O
about	O
biological	O
sequences	O
collected	O
from	O
the	O
environment	O
Windows	B-Application
,	O
macOS	B-Application
GPL	B-License
Collaborative	O
project	O
Genomespace	B-Application
Centralized	O
web	O
application	O
that	O
provides	O
data	O
format	O
transformations	O
and	O
facilitates	O
connections	O
with	O
other	O
bioinformatics	O
tools	O
Web	B-Application
browser	I-Application
LGPL	B-Application
Broad	O
Institute	O
,	O
collaborative	O
project	O
GENtle	B-Language
An	O
equivalent	O
to	O
the	O
proprietary	O
Vector	B-Application
NTI	I-Application
,	O
a	O
tool	O
to	O
analyze	O
and	O
edit	O
DNA	O
sequence	O
files	O
GPL	B-License
Magnus	O
Manske	O
GROMACS	B-Application
Molecular	O
dynamics	O
package	O
mainly	O
designed	O
for	O
simulations	O
of	O
proteins	O
,	O
lipids	O
and	O
nucleic	O
acids	O
.	O
</s>
<s>
Linux	B-Application
,	O
macOS	B-Application
,	O
Windows	B-Application
Common	O
Public	O
1.0	O
GenoViz	O
Integrated	B-Application
Genome	I-Application
Browser	I-Application
Java-based	O
desktop	O
genome	O
browser	B-Application
Linux	B-Application
,	O
macOS	B-Application
,	O
Windows	B-Application
Common	O
Public	O
1.0	O
GenoViz	O
InterMine	O
Extensive	O
data	O
warehouse	O
system	O
for	O
the	O
analysis	O
and	O
integration	O
of	O
biological	O
datasets	O
written	O
in	O
Java	B-Device
and	O
JavaScript	B-Language
Cross-platform	B-Operating_System
LGPL	B-Application
University	O
of	O
Cambridge	O
LabKey	B-Application
Server	I-Application
Software	O
platform	O
,	O
allows	O
organizations	O
to	O
integrate	O
,	O
analyze	O
,	O
and	O
share	O
complex	O
biomedical	O
data	O
Linux	B-Application
,	O
macOS	B-Application
,	O
Windows	B-Application
Apache	B-Application
LabKey	O
Software	O
Foundation	O
LAMMPS	B-Application
Molecular	O
dynamics	O
program	O
written	O
in	O
C++	B-Language
Linux	B-Application
,	O
macOS	B-Application
,	O
Windows	B-Application
Apache	B-Application
Sandia	O
National	O
Laboratories	O
.	O
</s>
<s>
mothur	B-Application
Software	O
for	O
analysis	O
of	O
16S	O
rRNA	O
gene	O
amplicon	O
sequence	O
data	O
Linux	B-Application
,	O
macOS	B-Application
,	O
Windows	B-Application
GPL	B-License
University	O
of	O
Michigan	O
PathVisio	B-Language
Desktop	O
software	O
for	O
drawing	O
,	O
analyzing	O
,	O
and	O
visualizing	O
biological	O
pathways	O
Linux	B-Application
,	O
macOS	B-Application
,	O
Windows	B-Application
Apache	B-Application
2.0	O
Maastricht	O
University	O
Orange	B-Application
Component-based	O
data	B-Application
mining	I-Application
and	O
machine	O
learning	O
software	O
suite	O
written	O
in	O
C++	B-Language
,	O
featuring	O
a	O
visual	O
programming	O
front-end	O
for	O
exploratory	B-General_Concept
data	I-General_Concept
analysis	I-General_Concept
and	O
interactive	O
visualization	O
,	O
and	O
Python	B-Language
bindings	O
and	O
libraries	O
for	O
scripting	O
Linux	B-Application
,	O
macOS	B-Application
,	O
Windows	B-Application
GPL	B-License
University	O
of	O
Ljubljana	O
SAMtools	B-Application
Utilities	O
for	O
interacting	O
with	O
high-throughput	O
sequencing	O
data	O
and	O
alignments	O
in	O
sam/bam	O
format	O
Unix/Linux	O
MIT	B-License
Collaborative	O
projectSOAP	O
SuiteSuite	O
of	O
tools	O
for	O
assembly	O
,	O
alignment	O
,	O
and	O
analysis	O
of	O
short	O
read	O
next	O
generation	O
sequencing	O
dataUnix/Linux	O
,	O
macOSGPLBGI	O
Staden	B-Application
Package	I-Application
Sequence	O
assembly	O
,	O
editing	O
,	O
and	O
analysis	O
,	O
mainly	O
consisting	O
of	O
gap4	O
,	O
gap5	O
,	O
and	O
spin	O
.	O
</s>
<s>
Written	O
in	O
C	O
,	O
C++	B-Language
,	O
Fortran	O
and	O
Tcl	O
.	O
</s>
