<s>
This	O
page	O
is	O
a	O
subsection	O
of	O
the	O
list	B-Application
of	I-Application
sequence	I-Application
alignment	I-Application
software	I-Application
.	O
</s>
<s>
Name	O
Structure	O
prediction	O
tools	O
integrated	O
Can	O
align	O
sequences	O
Can	O
calculate	O
phylogenetic	O
trees	O
Other	O
features	O
Format	O
support	O
LicenseCan	O
run	O
on	O
BrowserOperating	O
Platforms	O
Link	O
Alan	O
Allows	O
sequence	O
alignments	O
to	O
be	O
viewed	O
quickly	O
and	O
directly	O
in	O
a	O
linux	O
terminal	O
without	O
X-forwarding	O
FASTA	B-Application
,	O
Clustal	B-Application
,	O
GPL	B-License
3NoLinux	O
Terminal	O
Ale	O
(	O
emacs	B-Application
plugin	O
)	O
GenBank	O
,	O
EMBL	O
,	O
FASTA	B-Application
,	O
PHYLIP	B-Application
,	O
GPLNoGNU	O
Emacs	B-Application
AliView	O
2021	O
Fast	O
,	O
easy	O
navigation	O
through	O
unlimited	O
mouse	O
wheel	O
zoom	O
in-out	O
feature	O
.	O
</s>
<s>
FASTA	B-Application
,	O
FASTQ	O
,	O
PHYLIP	B-Application
,	O
Nexus	O
,	O
MSF	O
,	O
Clustal	B-Application
,	O
GPL	B-License
3	O
?	O
Cross-platform	O
-Mac	O
OS	O
,	O
</s>
<s>
FASTA	B-Application
,	O
PHYLIP	B-Application
,	O
Nexus	O
,	O
Clustal	B-Application
,	O
Stockholm	O
,	O
GPL	B-License
3	O
NoCross-platform	O
,	O
see	O
also	O
arb	O
Edits	O
huge	O
alignments	O
and	O
trees	O
.	O
</s>
<s>
FASTA	B-Application
,	O
GenBank	O
,	O
EMBL	O
,	O
Newick	B-Data_Structure
,	O
freeware	B-License
,	O
arb	O
license	B-License
,	O
open	O
modifiable	O
source	O
NoLinux	O
,	O
Mac	O
OS	O
(	O
homebrew	O
)	O
Base-By-Base	O
Visual	O
summary	O
,	O
percent	O
identity	O
tables	O
,	O
some	O
integrated	O
advanced	O
analysis	O
tools	O
Genbank	O
,	O
FASTA	B-Application
,	O
EMBEL	O
,	O
Clustal	B-Application
,	O
base-by-base	O
files	O
,	O
freeware	B-License
,	O
must	O
register	O
??	O
</s>
<s>
BioEdit	O
Plasmid	O
drawing	O
,	O
ABI	O
chromatograms	O
,	O
Genbank	O
,	O
FASTA	B-Application
,	O
PHYLIP	B-Application
3.2	O
and	O
4	O
,	O
NBRF-PIR	O
,	O
freewareNoWindows	O
(	O
95/98/NT/2000/XP	O
)	O
BioNumerics	B-Application
Genbank	O
,	O
FASTA	B-Application
,	O
commercial	B-Application
??	O
</s>
<s>
bioSyntax	O
Native	O
syntax	O
highlighting	O
support	O
for	O
Vim	B-Application
,	O
less	O
,	O
gedit	B-Language
and	O
Sublime	O
FASTA	B-Application
,	O
FASTQ	O
,	O
Clustal	B-Application
,	O
SAM	B-Application
,	O
VCF	O
and	O
more	O
,	O
GPL	B-License
3NoVim	O
,	O
Less	O
,	O
GEdit	B-Language
,	O
&	O
Sublime	O
BoxShade	O
Specifically	O
for	O
multiple	O
alignments	O
MSF	O
format	O
as	O
written	O
by	O
PILEUP	O
,	O
READSEQ	O
,	O
or	O
SEQIO	O
(	O
fmtseq	O
)	O
;	O
ALN	O
format	O
as	O
written	O
by	O
ClustalW	B-Application
,	O
public	O
domainNoMSDOS	O
,	O
VMS	O
CINEMA	O
,	O
but	O
can	O
read-show	O
2D	O
structure	O
annotations	O
Dotplot	O
,	O
6	O
frame	O
translation	O
,	O
Blast	O
Nexus	O
,	O
MSF	O
,	O
Clustal	B-Application
,	O
FASTA	B-Application
,	O
PHYLIP	B-Application
,	O
PIR	O
,	O
PRINTS	O
,	O
freewareNoCross-platform	O
-Mac	O
OS	O
,	O
Linux	O
,	O
Windows	O
CLC	O
viewer	O
(	O
free	O
version	O
)	O
Workflows	O
,	O
blast-genbank	O
search	O
many	O
,	O
freeware	B-License
.	O
</s>
<s>
More	O
options	O
available	O
in	O
commercial	B-Application
versions.No	O
?	O
</s>
<s>
Publication	O
ClustalX	B-Application
viewer	O
Alignment	O
quality	O
analysis	O
Nexus	O
,	O
MSF	O
,	O
Clustal	B-Application
,	O
FASTA	B-Application
,	O
PHYLIP	B-Application
,	O
freeware	B-License
for	O
academic	O
useNoCommand	O
line	O
Cylindrical	O
Alignment	O
App	O
3D	O
,	O
animation	O
,	O
drilldown	O
,	O
legend	O
selection	O
BLAST	O
XML	O
,	O
proprietary	O
XML	O
,	O
GFF3	O
,	O
ClustalW	B-Application
,	O
INSDSet	O
,	O
user	O
expandable	O
with	O
XSLT	B-Application
,	O
CDDL	B-Application
1	I-Application
.	I-Application
</s>
<s>
?	O
Cross-platform	O
-Mac	O
OS	O
,	O
Linux	O
,	O
Windows	O
Cylindrical	O
BLAST	O
Viewer	O
3D	O
,	O
animation	O
,	O
drilldown	O
,	O
legend	O
selection	O
BLAST	O
XML	O
,	O
proprietary	O
XML	O
,	O
GFF3	O
,	O
ClustalW	B-Application
,	O
INSDSet	O
,	O
user	O
expandable	O
with	O
XSLT	B-Application
,	O
GPL	B-License
??	O
</s>
<s>
DECIPHER	O
Primer-Probe	O
design	O
,	O
Chimera	O
finding	O
FASTA	B-Application
,	O
FASTQ	O
,	O
GenBank	O
,	O
GPLNoMac	O
OS	O
,	O
Windows	O
Discovery	O
Studio	O
Visualizer	O
supports	O
2D	O
and	O
3D	O
structure	O
and	O
sequence	O
;	O
full	O
version	O
has	O
comprehensive	O
functionality	O
for	O
protein	O
,	O
nucleotides	O
,	O
more	O
BSML	O
,	O
EMBL	O
,	O
GB	O
,	O
HELM	O
,	O
Clustal	B-Application
,	O
FASTA	B-Application
,	O
GDE	O
,	O
PDB	O
,	O
SEQ	O
,	O
SPT	O
,	O
...	O
,	O
commercial	B-Application
,	O
Viewer	O
is	O
Freeware	B-License
?	O
Linux	O
,	O
Windows	O
DnaSP	O
Can	O
compute	O
several	O
population	O
genetics	O
statistics	O
,	O
reconstruct	O
haplotypes	O
with	O
PHASE	O
FASTA	B-Application
,	O
Nexus	O
,	O
MEGA	B-Application
,	O
PHYLIP	B-Application
,	O
commercial	B-Application
,	O
freeware	B-License
for	O
noncommercial	O
use	O
?	O
Cross-platform	O
-Mac	O
OS	O
,	O
Linux	O
,	O
Windows	O
DNASTAR	O
Lasergene	O
Molecular	O
Biology	O
Suite	O
Align	O
DNA	O
,	O
RNA	O
,	O
protein	O
,	O
or	O
DNA	O
+	O
protein	O
sequences	O
via	O
a	O
variety	O
of	O
pairwise	O
and	O
multiple	O
sequence	O
alignment	O
algorithms	O
,	O
generate	O
phylogenetic	O
trees	O
to	O
predict	O
evolutionary	O
relationships	O
,	O
explore	O
sequence	O
tracks	O
to	O
view	O
GC	O
content	O
,	O
gap	O
fraction	O
,	O
sequence	O
logos	O
,	O
translation	O
ABI	O
,	O
DNA	O
Multi-Seq	O
,	O
FASTA	B-Application
,	O
GCG	O
Pileup	O
,	O
GenBank	O
,	O
Phred	O
,	O
commercial	B-Application
,	O
academic	O
licenses	O
available	O
?	O
Mac	O
OS	O
,	O
Windows	O
emacs	B-Application
-	O
biomode	O
,	O
GPL	B-License
??	O
</s>
<s>
FLAK	O
Very	O
fast	O
,	O
highly	O
customisable	O
,	O
visualisation	O
is	O
WYSIWYG	O
with	O
filtering	O
and	O
fuzzy	O
options	O
FASTA	B-Application
,	O
commercial	B-Application
,	O
freeware	B-License
for	O
noncommercial	O
use	O
??	O
</s>
<s>
Genedoc	O
,	O
but	O
can	O
read-show	O
annotations	O
,	O
but	O
can	O
read-show	O
annotations	O
gel	O
simulation	O
,	O
stats	O
,	O
multiple	O
views	O
,	O
simple	O
many	O
,	O
freeware	B-License
??	O
</s>
<s>
table	O
of	O
features	O
Geneious	O
-	O
powered	O
by	O
EMBOSS	B-Application
tools	O
Whole	O
genome	O
assembly	O
,	O
restriction	O
analysis	O
,	O
cloning	O
,	O
primer	O
design	O
,	O
dotplot	O
,	O
much	O
more	O
>40	O
file	O
formats	O
imported	O
and	O
exported	O
,	O
commercial	B-Application
;	O
personal	O
,	O
floating	O
?	O
Cross-platform	O
-	O
Mac	O
,	O
Windows	O
,	O
Linux	O
Integrated	B-Application
Genome	I-Application
Browser	I-Application
(	O
IGB	O
)	O
Sequences	O
and	O
features	O
from	O
files	O
,	O
URLs	O
,	O
and	O
arbitrary	O
DAS	O
and	O
QuickLoad	O
servers	O
BAM	B-Application
,	O
FASTA	B-Application
,	O
PSL	O
,	O
CPL	O
?	O
Cross-platform	O
-	O
Mac	O
,	O
Windows	O
,	O
Linux	O
interactive	O
Tree	O
Of	O
Life	O
(	O
iTOL	O
)	O
Phylogenetic	O
tree	O
viewer-annotation	O
tool	O
which	O
can	O
visualise	O
alignments	O
directly	O
on	O
the	O
tree	O
.	O
</s>
<s>
FASTA	B-Application
,	O
free	O
useYesBrowser	O
IVisTMSA	O
Software	O
is	O
package	O
of	O
7	O
interactive	O
visual	O
tools	O
for	O
multiple	O
sequence	O
alignments	O
.	O
</s>
<s>
Includes	O
MSApad	O
,	O
MSA	O
comparator	O
,	O
MSA	O
reconstruction	O
tool	O
,	O
FASTA	B-Application
generator	O
and	O
MSA	O
ID	O
matrix	O
calculator	O
ClustalW	B-Application
,	O
MSF	O
,	O
PHYLIP	B-Application
,	O
PIR	O
,	O
GDE	O
,	O
Nexus	O
,	O
freeware	B-License
??	O
</s>
<s>
Structure/model	O
data	O
retrieval	O
from	O
PDB	O
and	O
3D-Beacons	O
including	O
PDBe	O
,	O
AlphaFold	O
DB	O
,	O
SWISS-MODEL	B-Application
.	O
</s>
<s>
FASTA	B-Application
,	O
Pfam	O
,	O
MSF	O
,	O
Clustal	B-Application
,	O
BLC	O
,	O
PIR	O
,	O
Stockholm	O
,	O
VCF	O
,	O
AMSA	O
,	O
BioJSON	O
,	O
Clustal	B-Application
,	O
ENA	O
,	O
GenBank	O
,	O
GFF2	O
,	O
GFF3	O
,	O
JnetFile	O
,	O
PHYLIP	B-Application
,	O
PileUp	O
,	O
RNAML	O
,	O
CIF	O
,	O
mmCIF	O
,	O
PDB	O
.	O
</s>
<s>
FASTA	B-Application
,	O
MSF	O
,	O
Clustal	B-Application
,	O
PHYLIP	B-Application
,	O
Newick	B-Data_Structure
,	O
PDB	O
,	O
commercial	B-Application
,	O
freeware	B-License
for	O
academic	O
use	O
?	O
Cross-platform	O
-Mac	O
OS	O
,	O
Linux	O
,	O
</s>
<s>
Windows	O
manual	O
JSAV	O
A	O
JavaScript	O
component	O
allowing	O
integrating	O
an	O
alignment	O
viewer	O
into	O
web	O
pages	O
An	O
array	O
of	O
JavaScript	O
objects	O
,	O
GPL	B-License
2YesBrowser	O
Lucid	O
Align	O
Native	O
desktop	O
alignment	O
viewer	O
,	O
uses	O
trackpad/mouse	O
gestures	O
.	O
</s>
<s>
Allows	O
streaming	O
remote	O
data	O
BAM	B-Application
,	O
FASTQ	O
,	O
FASTA	B-Application
,	O
commercial	B-Application
,	O
freeware	B-License
for	O
academic	O
useNoMac	O
OS	O
Maestro	O
Mapping	O
from	O
sequence	O
to	O
3D	O
structure	O
,	O
structure-sequence	O
editing-modeling	O
Clustal	B-Application
,	O
FASTA	B-Application
PDB	O
,	O
freeware	B-License
for	O
academic	O
use	O
??	O
</s>
<s>
MEGA	B-Application
Extended	O
support	O
to	O
phylogenetics	O
analysis	O
FASTA	B-Application
,	O
Clustal	B-Application
,	O
Nexus	O
,	O
MEGA	B-Application
,	O
etc	O
.	O
</s>
<s>
,	O
freeware	B-License
,	O
must	O
register	O
??	O
</s>
<s>
Molecular	B-Application
Operating	I-Application
Environment	I-Application
(	O
MOE	O
)	O
Part	O
of	O
an	O
extensive	O
collection	O
of	O
applications	O
for	O
sequence	O
to	O
structure	O
,	O
including	O
homology	O
modelling	O
;	O
3D	O
visualisation	O
,	O
etc	O
.	O
</s>
<s>
Clustal	B-Application
,	O
FASTA	B-Application
,	O
PDB	O
,	O
EMBL	O
,	O
GCG	O
,	O
GCG_MSF	O
,	O
Genbank	O
,	O
PHYLIP	B-Application
,	O
PIR	O
,	O
raw_seq	O
?	O
</s>
<s>
FASTA	B-Application
,	O
Creative	O
Commons	O
Attribution	O
NonCommercial	O
Share-alike	O
??	O
</s>
<s>
Multiseq	O
(	O
VMD	B-Application
plugin	O
)	O
,	O
but	O
can	O
display	O
and	O
align	O
3D	O
structures	O
Scripting	O
via	O
Tcl	B-Operating_System
,	O
mapping	O
from	O
sequence	O
to	O
3D	O
structure	O
FASTA	B-Application
,	O
PDB	O
,	O
ALN	O
,	O
PHYLIP	B-Application
,	O
NEXUS	O
,	O
freeware	B-License
,	O
but	O
VMD	B-Application
is	O
free	O
for	O
noncommercial	O
use	O
only	O
??	O
</s>
<s>
MView	O
Stacked	O
alignments	O
from	O
blast	O
and	O
fasta	B-Application
suites	O
,	O
various	O
MSA	O
format	O
conversions	O
,	O
HTML	O
markup	O
,	O
consensus	O
patterns	O
BLAST	O
search	O
,	O
FASTA	B-Application
search	O
,	O
Clustal	B-Application
,	O
HSSP	O
,	O
FASTA	B-Application
,	O
PIR	O
,	O
MSF	O
,	O
GPLNoCross-platform	O
-	O
Mac	O
OS	O
,	O
Linux	O
,	O
Windows	O
PFAAT	O
,	O
but	O
can	O
display	O
3D	O
structures	O
Manual	O
annotation	O
,	O
conservation	O
scores	O
Nexus	O
,	O
MSF	O
,	O
Clustal	B-Application
,	O
FASTA	B-Application
,	O
PFAAT	O
,	O
freeware	B-License
??	O
</s>
<s>
Ralee	O
(	O
emacs	B-Application
plugin	O
for	O
RNA	O
al	O
.	O
</s>
<s>
editing	O
)	O
Stockholm	O
,	O
GPL	B-License
??	O
</s>
<s>
S2S	O
RNA	O
editor	O
Base-base	O
interactions	O
,	O
2D-3D	O
viewer	O
FASTA	B-Application
,	O
RnaML	O
,	O
freeware	B-License
??	O
</s>
<s>
Seaview	O
Dot-plot	O
,	O
vim-like	O
editing	O
keys	O
Nexus	O
,	O
MSF	O
,	O
Clustal	B-Application
,	O
FASTA	B-Application
,	O
PHYLIP	B-Application
,	O
MASE	O
,	O
freeware	B-License
??	O
</s>
<s>
Seqotron	O
Manual	O
alignment	O
,	O
tree	O
visualisation	O
Nexus	O
,	O
Clustal	B-Application
,	O
FASTA	B-Application
,	O
PHYLIP	B-Application
,	O
MEGA	B-Application
,	O
Stockholm	O
,	O
NBRF/PIR	O
,	O
GDE	O
flat	O
,	O
GPL	B-License
?	O
Mac	O
OS	O
X	O
publication	O
Sequilab	O
Link	O
alignment	O
results	O
to	O
analysis	O
tools	O
(	O
Primer	O
design	O
,	O
Gel	O
mobility	O
and	O
Maps	O
,	O
Plasmapper	O
,	O
siRNA	O
design	O
Epitope	O
prediction	O
)	O
,	O
Save	O
research	O
logs	O
,	O
Create	O
custom	O
toolbars	O
Accession	O
number	O
,	O
GI	O
number	O
,	O
PDB	O
ID	O
,	O
FASTA	B-Application
,	O
drag-drop	O
from	O
external	O
URL	O
from	O
within	O
the	O
user	O
interface	O
,	O
freeware	B-License
??	O
</s>
<s>
SeqPup	O
,	O
freeware	B-License
??	O
</s>
<s>
Sequlator	O
easy	O
alignment	O
editing	O
MSF	O
,	O
freeware	B-License
??	O
</s>
<s>
SnipViz	O
(	O
but	O
can	O
display	O
them	O
)	O
Pure	O
Javascript	O
and	O
HTML	O
;	O
suitable	O
to	O
integrate	O
in	O
websites	O
FASTA	B-Application
,	O
newick	B-Data_Structure
,	O
Apache	B-Application
2.0YesBrowsers	O
,	O
publication	O
Strap	O
Dot-plot	O
,	O
structure-neighbors	O
,	O
3D-superposition	O
,	O
Blast-search	O
,	O
Mutation-SNP	O
analysis	O
,	O
Sequence	O
features	O
,	O
BioJava-interface	O
MSF	O
,	O
Stockholm	O
,	O
ClustalW	B-Application
,	O
Nexus	O
,	O
FASTA	B-Application
,	O
PDB	O
,	O
Embl	O
,	O
GenBank	O
,	O
hssp	O
,	O
Pfam	O
,	O
GPL	B-License
??	O
</s>
<s>
ACE	O
,	O
AFG	O
,	O
MAQ	O
,	O
SOAP2	O
,	O
SAM	B-Application
,	O
BAM	B-Application
,	O
FASTA	B-Application
,	O
FASTQ	O
,	O
GFF3	O
,	O
BSD	B-Operating_System
2-clause	O
??	O
</s>
<s>
UGENE	B-Language
Many	O
FASTA	B-Application
,	O
FASTQ	O
,	O
GenBank	O
,	O
EMBL	O
,	O
ABIF	O
,	O
SCF	O
,	O
ClustalW	B-Application
,	O
Stockholm	O
,	O
Newick	B-Data_Structure
,	O
PDB	O
,	O
MSF	O
,	O
GFF	O
,	O
GPL	B-License
??	O
</s>
<s>
VISSA	O
sequence-structure	O
viewer	O
Mapping	O
from	O
sequence	O
to	O
3D	O
structure	O
Clustal	B-Application
,	O
FASTA	B-Application
,	O
freeware	B-License
??	O
</s>
<s>
DNApy	O
Editing	O
of	O
GenBank	O
files	O
,	O
plasmid	O
drawing	O
,	O
ABI	O
chromatograms	O
,	O
FASTA	B-Application
,	O
FASTQ	O
,	O
GenBank	O
,	O
GPL	B-License
3	O
??	O
</s>
