<s>
This	O
list	B-Application
of	I-Application
sequence	I-Application
alignment	I-Application
software	I-Application
is	O
a	O
compilation	O
of	O
software	O
tools	O
and	O
web	O
portals	O
used	O
in	O
pairwise	O
sequence	B-Algorithm
alignment	I-Algorithm
and	O
multiple	O
sequence	B-Algorithm
alignment	I-Algorithm
.	O
</s>
<s>
See	O
structural	B-Application
alignment	I-Application
software	I-Application
for	O
structural	O
alignment	O
of	O
proteins	O
.	O
</s>
<s>
Name	O
Description	O
Sequence	O
type*	O
Authors	O
Year	O
BLAST	B-Application
Local	O
search	O
with	O
fast	O
k-tuple	O
heuristic	O
(	O
Basic	O
Local	B-Algorithm
Alignment	I-Algorithm
Search	O
Tool	O
)	O
Both	O
Altschul	O
SF	O
,	O
Gish	O
W	O
,	O
Miller	O
W	O
,	O
Myers	O
EW	O
,	O
Lipman	O
DJ	O
1990	O
HPC-BLAST	O
NCBI	O
compliant	O
multinode	O
and	O
multicore	O
BLAST	B-Application
wrapper	O
.	O
</s>
<s>
Distributed	O
with	O
the	O
latest	O
version	O
of	O
BLAST	B-Application
,	O
this	O
wrapper	O
facilitates	O
parallelization	O
of	O
the	O
algorithm	O
on	O
modern	O
hybrid	O
architectures	O
with	O
many	O
nodes	O
and	O
many	O
cores	O
within	O
each	O
node.HPC-BLAST	O
code	O
repository	O
https://github.com/UTennessee-JICS/HPC-BLAST	O
Protein	O
Burdyshaw	O
CE	O
,	O
Sawyer	O
S	O
,	O
Horton	O
MD	O
,	O
Brook	O
RG	O
,	O
Rekapalli	O
B	O
2017	O
CS-BLAST	B-Application
Sequence-context	O
specific	O
BLAST	B-Application
,	O
more	O
sensitive	O
than	O
BLAST	B-Application
,	O
FASTA	B-Application
,	O
and	O
SSEARCH	O
.	O
</s>
<s>
Position-specific	O
iterative	O
version	O
CSI-BLAST	B-Application
more	O
sensitive	O
than	O
PSI-BLAST	O
Protein	O
Angermueller	O
C	O
,	O
Biegert	O
A	O
,	O
Soeding	O
J	O
2013	O
CUDASW++	O
GPU	O
accelerated	O
Smith	B-Algorithm
Waterman	I-Algorithm
algorithm	I-Algorithm
for	O
multiple	O
shared-host	O
GPUs	O
Protein	O
Liu	O
Y	O
,	O
Maskell	O
DL	O
and	O
Schmidt	O
B	O
2009/2010	O
DIAMOND	O
BLASTX	O
and	O
BLASTP	O
aligner	O
based	O
on	O
double	O
indexing	O
Protein	O
Buchfink	O
B	O
,	O
Xie	O
C	O
,	O
Huson	O
DH	O
,	O
Reuter	O
K	O
,	O
Drost	O
HG	O
2015/2021	O
FASTA	B-Application
Local	O
search	O
with	O
fast	O
k-tuple	O
heuristic	O
,	O
slower	O
but	O
more	O
sensitive	O
than	O
BLAST	B-Application
Both	O
GGSEARCH	O
,	O
GLSEARCH	O
Global:Global	O
(	O
GG	O
)	O
,	O
Global:Local	O
(	O
GL	O
)	O
alignment	O
with	O
statistics	O
Protein	O
Genome	O
Magician	O
Software	O
for	O
ultra	O
fast	O
local	O
DNA	O
sequence	O
motif	O
search	O
and	O
pairwise	O
alignment	O
for	O
NGS	O
data	O
(	O
FASTA	B-Application
,	O
FASTQ	O
)	O
.	O
</s>
<s>
It	O
is	O
developed	O
in	O
Java	B-Language
and	O
open	O
source	O
.	O
</s>
<s>
Both	O
Albrecht	O
F	O
2015	O
HMMER	B-Language
Local	O
and	O
global	O
search	O
with	O
profile	O
Hidden	O
Markov	O
models	O
,	O
more	O
sensitive	O
than	O
PSI-BLAST	O
Both	O
Durbin	O
R	O
,	O
Eddy	O
SR	O
,	O
Krogh	O
A	O
,	O
Mitchison	O
G	O
1998	O
HH-suite	B-Application
Pairwise	O
comparison	O
of	O
profile	O
Hidden	O
Markov	O
models	O
;	O
very	O
sensitive	O
Protein	O
Söding	O
J	O
2005/2012	O
IDF	O
Inverse	O
Document	O
Frequency	O
Both	O
Infernal	O
Profile	O
SCFG	B-General_Concept
search	O
RNA	O
Eddy	O
S	O
KLAST	O
High-performance	O
general	O
purpose	O
sequence	B-Algorithm
similarity	I-Algorithm
search	I-Algorithm
tool	O
Both	O
2009/2014	O
LAMBDA	O
High	O
performance	O
local	O
aligner	O
compatible	O
to	O
BLAST	B-Application
,	O
but	O
much	O
faster	O
;	O
supports	O
SAM/BAM	O
Protein	O
Hannes	O
Hauswedell	O
,	O
Jochen	O
Singer	O
,	O
Knut	O
Reinert	O
2014	O
MMseqs2	O
Software	O
suite	O
to	O
search	O
and	O
cluster	O
huge	O
sequence	O
sets	O
.	O
</s>
<s>
Similar	O
sensitivity	O
to	O
BLAST	B-Application
and	O
PSI-BLAST	O
but	O
orders	O
of	O
magnitude	O
faster	O
Protein	O
Steinegger	O
M	O
,	O
Mirdita	O
M	O
,	O
Galiez	O
C	O
,	O
Söding	O
J	O
2017	O
USEARCH	O
Ultra-fast	O
sequence	O
analysis	O
tool	O
Both	O
publication	O
2010OSWALDOpenCL	O
Smith-Waterman	B-Algorithm
on	O
Altera	O
's	O
FPGA	O
for	O
Large	O
Protein	O
Databases	O
ProteinRucci	O
E	O
,	O
García	O
C	O
,	O
Botella	O
G	O
,	O
De	O
Giusti	O
A	O
,	O
Naiouf	O
M	O
,	O
Prieto-Matías	O
M2016	O
parasail	O
Fast	O
Smith-Waterman	B-Algorithm
search	O
using	O
SIMD	O
parallelization	O
Both	O
Daily	O
J	O
2015	O
PSI-BLAST	O
Position-specific	O
iterative	O
BLAST	B-Application
,	O
local	O
search	O
with	O
position-specific	O
scoring	O
matrices	O
,	O
much	O
more	O
sensitive	O
than	O
BLAST	B-Application
Protein	O
Altschul	O
SF	O
,	O
Madden	O
TL	O
,	O
Schäffer	O
AA	O
,	O
Zhang	O
J	O
,	O
Zhang	O
Z	O
,	O
Miller	O
W	O
,	O
Lipman	O
DJ	O
1997	O
PSI-Search	O
Combining	O
the	O
Smith-Waterman	B-Algorithm
search	O
algorithm	O
with	O
the	O
PSI-BLAST	O
profile	O
construction	O
strategy	O
to	O
find	O
distantly	O
related	O
protein	O
sequences	O
,	O
and	O
preventing	O
homologous	O
over-extension	O
errors	O
.	O
</s>
<s>
Wachtel2017	O
Bioconductor	B-Application
Biostrings::pairwiseAlignment	O
Dynamic	B-Algorithm
programming	I-Algorithm
Both	O
Both	O
+	O
Ends-free	O
P	O
.	O
Aboyoun	O
2008	O
BioPerl	B-Application
dpAlign	O
Dynamic	B-Algorithm
programming	I-Algorithm
Both	O
Both	O
+	O
Ends-free	O
Y	O
.	O
M	O
.	O
Chan	O
2003	O
BLASTZ	O
,	O
LASTZ	O
Seeded	O
pattern-matching	O
Nucleotide	O
Local	O
Schwartz	O
et	O
al	O
.	O
</s>
<s>
2004	O
,	O
2009	O
CUDAlign	O
DNA	O
sequence	B-Algorithm
alignment	I-Algorithm
of	O
unrestricted	O
size	O
in	O
single	O
or	O
multiple	O
GPUs	O
Nucleotide	O
Local	O
,	O
SemiGlobal	O
,	O
Global	O
E	O
.	O
Sandes	O
2011-2015	O
DNADot	O
Web-based	O
dot-plot	O
tool	O
Nucleotide	O
Global	O
R	O
.	O
Bowen	O
1998	O
DOTLET	O
Java-based	O
dot-plot	O
tool	O
Both	O
Global	O
M	O
.	O
Pagni	O
and	O
T	O
.	O
Junier	O
1998	O
FEAST	O
Posterior	O
based	O
local	O
extension	O
with	O
descriptive	O
evolution	O
model	O
Nucleotide	O
Local	O
A	O
.	O
K	O
.	O
Hudek	O
and	O
D	O
.	O
G	O
.	O
Brown	O
2010Genome	O
Compiler	O
Genome	O
CompilerAlign	O
chromatogram	O
files	O
(	O
.ab1	O
,	O
.scf	O
)	O
against	O
a	O
template	O
sequence	O
,	O
locate	O
errors	O
,	O
and	O
correct	O
them	O
instantly	O
.	O
</s>
<s>
NucleotideLocalGenome	O
Compiler	O
Corporation2014	O
G-PAS	O
GPU-based	O
dynamic	B-Algorithm
programming	I-Algorithm
with	O
backtracking	O
Both	O
Local	O
,	O
SemiGlobal	O
,	O
Global	O
W	O
.	O
Frohmberg	O
,	O
M	O
.	O
Kierzynka	O
et	O
al	O
.	O
</s>
<s>
2011	O
GapMis	O
Does	O
pairwise	O
sequence	B-Algorithm
alignment	I-Algorithm
with	O
one	O
gap	O
Both	O
SemiGlobal	O
K	O
.	O
Frousios	O
,	O
T	O
.	O
Flouri	O
,	O
C	O
.	O
S	O
.	O
Iliopoulos	O
,	O
K	O
.	O
Park	O
,	O
S	O
.	O
P	O
.	O
Pissis	O
,	O
G	O
.	O
Tischler	O
2012	O
Genome	O
Magician	O
Software	O
for	O
ultra	O
fast	O
local	O
DNA	O
sequence	O
motif	O
search	O
and	O
pairwise	O
alignment	O
for	O
NGS	O
data	O
(	O
FASTA	B-Application
,	O
FASTQ	O
)	O
.	O
</s>
<s>
DNA	O
Local	O
,	O
SemiGlobal	O
,	O
Global	O
Hepperle	O
D	O
(	O
www.sequentix.de	O
)	O
2020	O
GGSEARCH	O
,	O
GLSEARCH	O
Global:Global	O
(	O
GG	O
)	O
,	O
Global:Local	O
(	O
GL	O
)	O
alignment	O
with	O
statistics	O
Protein	O
Global	O
in	O
query	O
W	O
.	O
Pearson	O
2007	O
JAligner	B-Application
Java	B-Language
open-source	B-Application
implementation	O
of	O
Smith-Waterman	B-Algorithm
Both	O
Local	O
A	O
.	O
Moustafa	O
2005	O
K*Sync	O
Protein	O
sequence	O
to	O
structure	O
alignment	O
that	O
includes	O
secondary	O
structure	O
,	O
structural	O
conservation	O
,	O
structure-derived	O
sequence	O
profiles	O
,	O
and	O
consensus	O
alignment	O
scores	O
Protein	O
Both	O
D	O
.	O
Chivian	O
&	O
D	O
.	O
Baker	O
2003	O
LALIGN	O
Multiple	O
,	O
non-overlapping	O
,	O
local	O
similarity	O
(	O
same	O
algorithm	O
as	O
SIM	O
)	O
Both	O
Local	O
non-overlapping	O
W	O
.	O
Pearson	O
1991	O
(	O
algorithm	O
)	O
NW-align	O
Standard	O
Needleman-Wunsch	B-Algorithm
dynamic	B-Algorithm
programming	I-Algorithm
algorithm	O
Protein	O
Global	O
Y	O
Zhang	O
2012	O
mAlign	O
modelling	O
alignment	O
;	O
models	O
the	O
information	O
content	O
of	O
the	O
sequences	O
Nucleotide	O
Both	O
D	O
.	O
Powell	O
,	O
L	O
.	O
Allison	O
and	O
T	O
.	O
I	O
.	O
Dix	O
2004	O
matcher	O
Waterman-Eggert	O
local	B-Algorithm
alignment	I-Algorithm
(	O
based	O
on	O
LALIGN	O
)	O
Both	O
Local	O
I	O
.	O
Longden	O
(	O
modified	O
from	O
W	O
.	O
Pearson	O
)	O
1999	O
MCALIGN2	O
explicit	O
models	O
of	O
indel	O
evolution	O
DNA	O
Global	O
J	O
.	O
Wang	O
et	O
al	O
.	O
</s>
<s>
2006	O
MegAlign	O
Pro	O
(	O
Lasergene	O
Molecular	O
Biology	O
)	O
Software	O
to	O
align	O
DNA	O
,	O
RNA	O
,	O
protein	O
,	O
or	O
DNA	O
+	O
protein	O
sequences	O
via	O
pairwise	O
and	O
multiple	O
sequence	B-Algorithm
alignment	I-Algorithm
algorithms	O
including	O
MUSCLE	B-Application
,	O
Mauve	O
,	O
MAFFT	B-Application
,	O
Clustal	B-Application
Omega	I-Application
,	O
Jotun	O
Hein	O
,	O
Wilbur-Lipman	O
,	O
Martinez	O
Needleman-Wunsch	B-Algorithm
,	O
Lipman-Pearson	O
and	O
Dotplot	O
analysis	O
.	O
</s>
<s>
Both	O
Both	O
DNASTAR	O
1993-2016	O
MUMmer	O
suffix	B-Architecture
tree	I-Architecture
based	O
Nucleotide	O
Global	O
S	O
.	O
Kurtz	O
et	O
al	O
.	O
</s>
<s>
2004	O
needle	O
Needleman-Wunsch	B-Algorithm
dynamic	B-Algorithm
programming	I-Algorithm
Both	O
SemiGlobal	O
A	O
.	O
Bleasby	O
1999	O
Ngila	O
logarithmic	O
and	O
affine	O
gap	O
costs	O
and	O
explicit	O
models	O
of	O
indel	O
evolution	O
Both	O
Global	O
R	O
.	O
Cartwright	O
2007	O
NW	O
Needleman-Wunsch	B-Algorithm
dynamic	B-Algorithm
programming	I-Algorithm
Both	O
Global	O
A.C.R.	O
</s>
<s>
Martin	O
1990-2015	O
parasail	O
C/C	O
++	O
/Python/Java	O
SIMD	O
dynamic	B-Algorithm
programming	I-Algorithm
library	O
for	O
SSE	B-General_Concept
,	O
AVX2	O
Both	O
Global	O
,	O
Ends-free	O
,	O
Local	O
J	O
.	O
</s>
<s>
Daily	O
2015	O
Path	O
Smith-Waterman	B-Algorithm
on	O
protein	O
back-translation	O
graph	O
(	O
detects	O
frameshifts	O
at	O
protein	O
level	O
)	O
Protein	O
Local	O
M	O
.	O
Gîrdea	O
et	O
al	O
.	O
</s>
<s>
2009	O
PatternHunter	B-Application
Seeded	O
pattern-matching	O
Nucleotide	O
Local	O
B	O
.	O
Ma	O
et	O
al	O
.	O
</s>
<s>
2002	O
–	O
2004	O
ProbA	O
(	O
also	O
propA	O
)	O
Stochastic	O
partition	O
function	O
sampling	O
via	O
dynamic	B-Algorithm
programming	I-Algorithm
Both	O
Global	O
U	O
.	O
Mückstein	O
2002	O
PyMOL	O
"	O
align	O
"	O
command	O
aligns	O
sequence	O
&	O
applies	O
it	O
to	O
structure	O
Protein	O
Global	O
(	O
by	O
selection	O
)	O
W	O
.	O
L	O
.	O
DeLano	O
2007	O
REPuter	O
suffix	B-Architecture
tree	I-Architecture
based	O
Nucleotide	O
Local	O
S	O
.	O
Kurtz	O
et	O
al	O
.	O
</s>
<s>
2010	O
SEQALN	O
Various	O
dynamic	B-Algorithm
programming	I-Algorithm
Both	O
Local	O
or	O
global	O
M.S.	O
</s>
<s>
2004	O
,	O
freeware	B-License
for	O
education	O
,	O
research	O
,	O
nonprofit	O
ALE	O
manual	O
alignment	O
;	O
some	O
software	O
assistance	O
Nucleotides	O
Local	O
J	O
.	O
Blandy	O
and	O
K	O
.	O
Fogel	O
1994	O
(	O
latest	O
version	O
2007	O
)	O
,	O
GPL2ALLALIGNFor	O
DNA	O
,	O
RNA	O
and	O
protein	O
molecules	O
up	O
to	O
32MB	O
,	O
aligns	O
all	O
sequences	O
of	O
size	O
K	O
or	O
greater	O
,	O
MSA	O
or	O
within	O
a	O
single	O
molecule	O
.	O
</s>
<s>
Wachtel2017Free	O
AMAP	B-Application
Sequence	O
annealing	O
Both	O
Global	O
A	O
.	O
Schwartz	O
and	O
L	O
.	O
Pachter	O
2006	O
anon	O
.	O
</s>
<s>
fast	O
,	O
optimal	O
alignment	O
of	O
three	O
sequences	O
using	O
linear	O
gap	O
costs	O
Nucleotides	O
Global	O
D	O
.	O
Powell	O
,	O
L	O
.	O
Allison	O
and	O
T	O
.	O
I	O
.	O
Dix	O
2000	O
BAli-Phy	B-Application
Tree+	O
multi-alignment	O
;	O
probabilistic-Bayesian	O
;	O
joint	O
estimation	O
Both	O
+	O
Codons	O
Global	O
BD	O
Redelings	O
and	O
MA	O
Suchard	O
2005	O
(	O
latest	O
version	O
2018	O
)	O
,	O
GPL	B-License
Base-By-Base	O
Java-based	O
multiple	O
sequence	B-Algorithm
alignment	I-Algorithm
editor	O
with	O
integrated	O
analysis	O
tools	O
Both	O
Local	O
or	O
global	O
R	O
.	O
Brodie	O
et	O
al	O
.	O
</s>
<s>
2004	O
,	O
freeware	B-License
,	O
must	O
register	O
CHAOS	O
,	O
DIALIGN	O
Iterative	O
alignment	O
Both	O
Local	O
(	O
preferred	O
)	O
M	O
.	O
Brudno	O
and	O
B	O
.	O
Morgenstern	O
2003	O
ClustalW	B-Application
Progressive	O
alignment	O
Both	O
Local	O
or	O
global	O
Thompson	O
et	O
al	O
.	O
</s>
<s>
1994	O
,	O
LGPL	B-Application
CodonCode	B-General_Concept
Aligner	I-General_Concept
Multi-alignment	O
;	O
ClustalW	B-Application
&	O
Phrap	O
support	O
Nucleotides	O
Local	O
or	O
global	O
P	O
.	O
Richterich	O
et	O
al	O
.	O
</s>
<s>
2003	O
(	O
latest	O
version	O
2009	O
)	O
Compass	B-Language
COmparison	O
of	O
Multiple	O
Protein	B-Algorithm
sequence	I-Algorithm
Alignments	I-Algorithm
with	O
assessment	O
of	O
Statistical	O
Significance	O
Protein	O
Global	O
R.I.	O
Sadreyev	O
,	O
et	O
al	O
.	O
</s>
<s>
2009	O
DECIPHER	B-Application
Progressive-iterative	O
alignment	O
Both	O
Global	O
Erik	O
S	O
.	O
Wright	O
2014	O
,	O
GPL	B-License
DIALIGN-TX	O
and	O
DIALIGN-T	O
Segment-based	O
method	O
Both	O
Local	O
(	O
preferred	O
)	O
or	O
Global	O
A.R.Subramanian	O
2005	O
(	O
latest	O
version	O
2008	O
)	O
DNA	B-Algorithm
Alignment	I-Algorithm
Segment-based	O
method	O
for	O
intraspecific	O
alignments	O
Both	O
Local	O
(	O
preferred	O
)	O
or	O
Global	O
A.Roehl	O
2005	O
(	O
latest	O
version	O
2008	O
)	O
DNA	O
Baser	O
Sequence	O
Assembler	O
Multi-alignment	O
;	O
Full	O
automatic	O
sequence	B-Algorithm
alignment	I-Algorithm
;	O
Automatic	O
ambiguity	O
correction	O
;	O
Internal	O
base	O
caller	O
;	O
Command	O
line	O
seq	O
alignment	O
Nucleotides	O
Local	O
or	O
global	O
Heracle	O
BioSoft	O
SRL	O
2006	O
(	O
latest	O
version	O
2018	O
)	O
Commercial	B-Application
(	O
some	O
modules	O
are	O
freeware	B-License
)	O
DNADynamo	B-Application
linked	O
DNA	O
to	O
Protein	O
multiple	O
alignment	O
with	O
MUSCLE	B-Application
,	O
Clustal	B-Application
and	O
Smith-Waterman	B-Algorithm
Both	O
Local	O
or	O
global	O
DNADynamo	B-Application
2004	O
(	O
newest	O
version	O
2017	O
)	O
EDNA	O
Energy	O
Based	O
Multiple	O
Sequence	B-Algorithm
Alignment	I-Algorithm
for	O
DNA	O
Binding	O
Sites	O
Nucleotides	O
Local	O
or	O
global	O
Salama	O
,	O
RA	O
.	O
</s>
<s>
2013	O
FAMSAProgressive	O
alignment	O
for	O
extremely	O
large	O
protein	O
families	O
(	O
hundreds	O
of	O
thousands	O
of	O
members	O
)	O
ProteinGlobalDeorowicz	O
et	O
al.2016	O
,	O
GPL	B-License
3	O
FSA	O
Sequence	O
annealing	O
Both	O
Global	O
R	O
.	O
K	O
.	O
Bradley	O
et	O
al	O
.	O
</s>
<s>
2008	O
Geneious	O
Progressive-Iterative	O
alignment	O
;	O
ClustalW	B-Application
plugin	O
Both	O
Local	O
or	O
global	O
A.J.	O
</s>
<s>
2005	O
(	O
latest	O
version	O
2017	O
)	O
GUIDANCE	O
Quality	O
control	O
and	O
filtering	O
of	O
multiple	O
sequence	B-Algorithm
alignments	I-Algorithm
Both	O
Local	O
or	O
global	O
O	O
.	O
Penn	O
et	O
al	O
.	O
</s>
<s>
Ranwez	O
et	O
al.2011	O
(	O
latest	O
version	O
,	O
v2.07	O
2023	O
)	O
MAFFT	B-Application
Progressive-iterative	O
alignment	O
Both	O
Local	O
or	O
global	O
K	O
.	O
Katoh	O
et	O
al	O
.	O
</s>
<s>
2005	O
,	O
BSD	B-Operating_System
MARNA	O
Multi-alignment	O
of	O
RNAs	O
RNA	O
Local	O
S	O
.	O
Siebert	O
et	O
al	O
.	O
</s>
<s>
2005	O
MAVID	B-Application
Progressive	O
alignment	O
Both	O
Global	O
N	O
.	O
Bray	O
and	O
L	O
.	O
Pachter	O
2004	O
MegAlign	O
Pro	O
(	O
Lasergene	O
Molecular	O
Biology	O
)	O
Software	O
to	O
align	O
DNA	O
,	O
RNA	O
,	O
protein	O
,	O
or	O
DNA	O
+	O
protein	O
sequences	O
via	O
pairwise	O
and	O
multiple	O
sequence	B-Algorithm
alignment	I-Algorithm
algorithms	O
including	O
MUSCLE	B-Application
,	O
Mauve	O
,	O
MAFFT	B-Application
,	O
Clustal	B-Application
Omega	I-Application
,	O
Jotun	O
Hein	O
,	O
Wilbur-Lipman	O
,	O
Martinez	O
Needleman-Wunsch	B-Algorithm
,	O
Lipman-Pearson	O
and	O
Dotplot	O
analysis	O
.	O
</s>
<s>
Both	O
Local	O
or	O
global	O
DNASTAR	O
1993-2016	O
MSA	O
Dynamic	B-Algorithm
programming	I-Algorithm
Both	O
Local	O
or	O
global	O
D.J.	O
</s>
<s>
1989	O
(	O
modified	O
1995	O
)	O
MSAProbs	O
Dynamic	B-Algorithm
programming	I-Algorithm
Protein	O
Global	O
Y	O
.	O
Liu	O
,	O
B	O
.	O
Schmidt	O
,	O
D	O
.	O
Maskell	O
2010	O
MULTALIN	O
Dynamic	O
programming-clustering	O
Both	O
Local	O
or	O
global	O
F	O
.	O
Corpet	O
1988	O
Multi-LAGAN	O
Progressive	O
dynamic	B-Algorithm
programming	I-Algorithm
alignment	O
Both	O
Global	O
M	O
.	O
Brudno	O
et	O
al	O
.	O
</s>
<s>
2003	O
MUSCLE	B-Application
Progressive-iterative	O
alignment	O
Both	O
Local	O
or	O
global	O
R	O
.	O
Edgar	O
2004	O
Opal	O
Progressive-iterative	O
alignment	O
Both	O
Local	O
or	O
global	O
T	O
.	O
Wheeler	O
and	O
J	O
.	O
Kececioglu	O
2007	O
(	O
latest	O
stable	O
2013	O
,	O
latest	O
beta	O
2016	O
)	O
Pecan	O
Probabilistic-consistency	O
DNA	O
Global	O
B	O
.	O
Paten	O
et	O
al	O
.	O
</s>
<s>
2008	O
Phylo	B-Operating_System
A	O
human	O
computing	O
framework	O
for	O
comparative	O
genomics	O
to	O
solve	O
multiple	O
alignment	O
Nucleotides	O
Local	O
or	O
global	O
McGill	O
Bioinformatics	O
2010	O
PMFastR	O
Progressive	O
structure	O
aware	O
alignment	O
RNA	O
Global	O
D	O
.	O
DeBlasio	O
,	O
J	O
Braund	O
,	O
S	O
Zhang	O
2009	O
Praline	O
Progressive-iterative-consistency-homology-extended	O
alignment	O
with	O
preprofiling	O
and	O
secondary	O
structure	O
prediction	O
Protein	O
Global	O
J	O
.	O
Heringa	O
1999	O
(	O
latest	O
version	O
2009	O
)	O
PicXAA	O
Nonprogressive	O
,	O
maximum	O
expected	O
accuracy	O
alignment	O
Both	O
Global	O
S.M.E.	O
</s>
<s>
Yoon	O
2010	O
POA	O
Partial	O
order/hidden	O
Markov	O
model	O
Protein	O
Local	O
or	O
global	O
C	O
.	O
Lee	O
2002	O
Probalign	B-Algorithm
Probabilistic/consistency	O
with	O
partition	O
function	O
probabilities	O
Protein	O
Global	O
Roshan	O
and	O
Livesay	O
2006	O
,	O
public	O
domain	O
ProbCons	O
Probabilistic/consistency	O
Protein	O
Local	O
or	O
global	O
C	O
.	O
Do	O
et	O
al	O
.	O
</s>
<s>
DNA/Protein	O
(	O
special	O
)	O
Local	O
or	O
global	O
Wernersson	O
and	O
Pedersen	O
2003	O
(	O
newest	O
version	O
2005	O
)	O
SAGA	O
Sequence	B-Algorithm
alignment	I-Algorithm
by	O
genetic	O
algorithm	O
Protein	O
Local	O
or	O
global	O
C	O
.	O
Notredame	O
et	O
al	O
.	O
</s>
<s>
1996	O
(	O
new	O
version	O
1998	O
)	O
SAM	B-Application
Hidden	O
Markov	O
model	O
Protein	O
Local	O
or	O
global	O
A	O
.	O
Krogh	O
et	O
al	O
.	O
</s>
<s>
2008	O
Stemloc	B-Application
Multiple	O
alignment	O
and	O
secondary	O
structure	O
prediction	O
RNA	O
Local	O
or	O
global	O
I	O
.	O
Holmes	O
2005	O
,	O
GPL	B-License
3	O
(	O
parte	O
de	O
DART	O
)	O
T-Coffee	B-Application
More	O
sensitive	O
progressive	O
alignment	O
Both	O
Local	O
or	O
global	O
C	O
.	O
Notredame	O
et	O
al	O
.	O
</s>
<s>
2000	O
(	O
newest	O
version	O
2008	O
)	O
,	O
GPL	B-License
2	O
UGENE	B-Language
Supports	O
multiple	O
alignment	O
with	O
MUSCLE	B-Application
,	O
KAlign	O
,	O
Clustal	B-Application
and	O
MAFFT	B-Application
plugins	O
Both	O
Local	O
or	O
global	O
UGENE	B-Language
team	O
2010	O
(	O
newest	O
version	O
2020	O
)	O
,	O
GPL	B-License
2	O
VectorFriends	O
VectorFriends	O
Aligner	O
,	O
MUSCLE	B-Application
plugin	O
,	O
and	O
ClustalW	B-Application
plugin	O
Both	O
Local	O
or	O
global	O
BioFriends	O
team	O
2013	O
,	O
freeware	B-License
for	O
academic	O
use	O
GLProbs	O
Adaptive	O
pair-Hidden	O
Markov	O
Model	O
based	O
approach	O
Protein	O
Global	O
Y	O
.	O
Ye	O
et	O
al	O
.	O
</s>
<s>
Name	O
Description	O
Sequence	O
type*	O
EAGLE	O
An	O
ultra-fast	O
tool	O
to	O
find	O
relative	O
absent	O
words	O
in	O
genomic	O
data	O
Nucleotide	O
ACT	O
(	O
Artemis	O
Comparison	O
Tool	O
)	O
Synteny	O
and	O
comparative	O
genomics	O
Nucleotide	O
AVID	O
Pairwise	O
global	O
alignment	O
with	O
whole	O
genomes	O
Nucleotide	O
BLAT	B-Application
Alignment	O
of	O
cDNA	O
sequences	O
to	O
a	O
genome	O
.	O
</s>
<s>
Nucleotide	O
DECIPHER	B-Application
Alignment	O
of	O
rearranged	O
genomes	O
using	O
6	O
frame	O
translation	O
Nucleotide	O
FLAK	O
Fuzzy	O
whole	O
genome	O
alignment	O
and	O
analysis	O
Nucleotide	O
GMAP	O
Alignment	O
of	O
cDNA	O
sequences	O
to	O
a	O
genome	O
.	O
</s>
<s>
Please	O
see	O
List	B-Application
of	I-Application
alignment	I-Application
visualization	I-Application
software	I-Application
.	O
</s>
<s>
Name	O
Description	O
paired-end	O
option	O
Use	O
FASTQ	O
quality	O
Gapped	O
Multi-threaded	O
License	O
Reference	O
Year	O
Arioc	O
Computes	O
Smith-Waterman	B-Algorithm
gapped	O
alignments	O
and	O
mapping	O
qualities	O
on	O
one	O
or	O
more	O
GPUs	O
.	O
</s>
<s>
,	O
BSD	B-Operating_System
2015	O
BarraCUDA	O
A	O
GPGPU	O
accelerated	O
Burrows	B-Algorithm
–	I-Algorithm
Wheeler	I-Algorithm
transform	I-Algorithm
(	O
FM-index	O
)	O
short	O
read	O
alignment	B-Application
program	I-Application
based	O
on	O
BWA	O
,	O
supports	O
alignment	O
of	O
indels	O
with	O
gap	O
openings	O
and	O
extensions	O
.	O
</s>
<s>
,	O
POSIX	B-Operating_System
Threads	I-Operating_System
and	O
CUDA	B-Architecture
,	O
GPL	B-License
BBMap	O
Uses	O
a	O
short	O
kmers	O
to	O
rapidly	O
index	O
genome	O
;	O
no	O
size	O
or	O
scaffold	O
count	O
limit	O
.	O
</s>
<s>
Performs	O
affine-transform-optimized	O
global	O
alignment	O
,	O
which	O
is	O
slower	O
but	O
more	O
accurate	O
than	O
Smith-Waterman	B-Algorithm
.	O
</s>
<s>
Pure	O
Java	B-Language
;	O
runs	O
on	O
any	O
platform	O
.	O
</s>
<s>
,	O
BSD	B-Operating_System
2010	O
BFAST	O
Explicit	O
time	O
and	O
accuracy	O
tradeoff	O
with	O
a	O
prior	O
accuracy	O
estimation	O
,	O
supported	O
by	O
indexing	O
the	O
reference	O
sequences	O
.	O
</s>
<s>
Performs	O
a	O
full	O
Smith	B-Algorithm
Waterman	I-Algorithm
alignment	O
.	O
</s>
<s>
,	O
POSIX	B-Operating_System
Threads	I-Operating_System
,	O
GPL	B-License
2009	O
BigBWA	O
Runs	O
the	O
Burrows	O
–	O
Wheeler	O
Aligner-BWA	O
on	O
a	O
Hadoop	B-Application
cluster	O
.	O
</s>
<s>
It	O
implies	O
an	O
important	O
reduction	O
in	O
the	O
computational	O
time	O
when	O
running	O
in	O
a	O
Hadoop	B-Application
cluster	O
,	O
adding	O
scalability	O
and	O
fault-tolerance	O
.	O
</s>
<s>
,	O
GPL	B-License
3	O
2015	O
BLASTN	O
BLAST	B-Application
's	O
nucleotide	O
alignment	B-Application
program	I-Application
,	O
slow	O
and	O
not	O
accurate	O
for	O
short	O
reads	O
,	O
and	O
uses	O
a	O
sequence	O
database	O
(	O
EST	O
,	O
Sanger	O
sequence	O
)	O
rather	O
than	O
a	O
reference	O
genome	O
.	O
</s>
<s>
BLAT	B-Application
Made	O
by	O
Jim	O
Kent	O
.	O
</s>
<s>
,	O
client-server	O
,	O
freeware	B-License
for	O
academic	O
and	O
noncommercial	O
use2002	O
Bowtie	B-Application
Uses	O
a	O
Burrows	B-Algorithm
–	I-Algorithm
Wheeler	I-Algorithm
transform	I-Algorithm
to	O
create	O
a	O
permanent	O
,	O
reusable	O
index	O
of	O
the	O
genome	O
;	O
1.3	O
GB	O
memory	O
footprint	O
for	O
human	O
genome	O
.	O
</s>
<s>
Supports	O
Maq-like	O
and	O
SOAP-like	O
alignment	O
policies	O
,	O
POSIX	B-Operating_System
Threads	I-Operating_System
,	O
Artistic2009	O
BWA	O
Uses	O
a	O
Burrows	B-Algorithm
–	I-Algorithm
Wheeler	I-Algorithm
transform	I-Algorithm
to	O
create	O
an	O
index	O
of	O
the	O
genome	O
.	O
</s>
<s>
It	O
's	O
a	O
bit	O
slower	O
than	O
Bowtie	B-Application
but	O
allows	O
indels	O
in	O
alignment	O
.	O
</s>
<s>
,	O
GPL	B-License
2009	O
BWA-PSSM	O
A	O
probabilistic	O
short	O
read	O
aligner	O
based	O
on	O
the	O
use	O
of	O
position	O
specific	O
scoring	O
matrices	O
(	O
PSSM	O
)	O
.	O
</s>
<s>
,	O
GPL	B-License
2014	O
CASHX	O
Quantify	O
and	O
manage	O
large	O
quantities	O
of	O
short-read	O
sequence	O
data	O
.	O
</s>
<s>
,	O
freeware	B-License
for	O
academic	O
and	O
noncommercial	O
use	O
Cloudburst	O
Short-read	O
mapping	O
using	O
Hadoop	B-Application
MapReduce	B-Operating_System
,	O
Hadoop	B-Application
MapReduce	B-Operating_System
,	O
Artistic	B-License
CUDA-EC	O
Short-read	O
alignment	O
error	O
correction	O
using	O
GPUs	O
.	O
</s>
<s>
,	O
GPU	O
enabledCUSHAW	O
A	O
CUDA	B-Architecture
compatible	O
short	O
read	O
aligner	O
to	O
large	O
genomes	O
based	O
on	O
Burrows	B-Algorithm
–	I-Algorithm
Wheeler	I-Algorithm
transform	I-Algorithm
(	O
GPU	O
enabled	O
)	O
,	O
GPL2012CUSHAW2	O
Gapped	O
short-read	O
and	O
long-read	O
alignment	O
based	O
on	O
maximal	O
exact	O
match	O
seeds	O
.	O
</s>
<s>
,	O
GPL	B-License
2014CUSHAW2-GPU	O
GPU-accelerated	O
CUSHAW2	O
short-read	O
aligner	O
.	O
</s>
<s>
,	O
GPL	B-License
CUSHAW3	O
Sensitive	O
and	O
accurate	O
base-space	O
and	O
color-space	O
short-read	O
alignment	O
with	O
hybrid	O
seeding	O
,	O
GPL	B-License
2012	O
drFAST	O
Read	O
mapping	O
alignment	O
software	O
that	O
implements	O
cache	O
obliviousness	O
to	O
minimize	O
main/cache	O
memory	O
transfers	O
like	O
mrFAST	O
and	O
mrsFAST	O
,	O
however	O
designed	O
for	O
the	O
SOLiD	O
sequencing	O
platform	O
(	O
color	O
space	O
reads	O
)	O
.	O
</s>
<s>
,	O
for	O
structural	O
variation	O
,	O
BSD	B-Operating_System
ELAND	O
Implemented	O
by	O
Illumina	O
.	O
</s>
<s>
Multithreading	O
and	O
MPI-enabled	O
,	O
GPL	B-License
3GASSST	O
Finds	O
global	O
alignments	O
of	O
short	O
DNA	O
sequences	O
against	O
large	O
DNA	O
banks	O
Multithreading	O
CeCILL	B-License
version	I-License
2	I-License
License	O
.	O
</s>
<s>
More	O
accurate	O
and	O
several	O
times	O
faster	O
than	O
BWA	O
or	O
Bowtie	B-Application
1/2	O
.	O
</s>
<s>
,	O
commercial	B-Application
GensearchNGS	O
Complete	O
framework	O
with	O
user-friendly	O
GUI	O
to	O
analyse	O
NGS	O
data	O
.	O
</s>
<s>
,	O
freeware	B-License
for	O
academic	O
and	O
noncommercial	O
useGNUMAP	O
Accurately	O
performs	O
gapped	O
alignment	O
of	O
sequence	O
data	O
obtained	O
from	O
next-generation	O
sequencing	O
machines	O
(	O
specifically	O
of	O
Solexa-Illumina	O
)	O
back	O
to	O
a	O
genome	O
of	O
any	O
size	O
.	O
</s>
<s>
,	O
also	O
supports	O
Illumina	O
*	O
_int.txt	O
and	O
*	O
_prb.txt	O
files	O
with	O
all	O
4	O
quality	O
scores	O
for	O
each	O
base	O
Multithreading	O
and	O
MPI-enabled	O
2009	O
HIVE-hexagon	O
Uses	O
a	O
hash	B-Algorithm
table	I-Algorithm
and	O
bloom	O
matrix	O
to	O
create	O
and	O
filter	O
potential	O
positions	O
on	O
the	O
genome	O
.	O
</s>
<s>
It	O
is	O
faster	O
than	O
Bowtie	B-Application
and	O
BWA	O
and	O
allows	O
indels	O
and	O
divergent	O
sensitive	O
alignments	O
on	O
viruses	O
,	O
bacteria	O
,	O
and	O
more	O
conservative	O
eukaryotic	O
alignments	O
.	O
</s>
<s>
,	O
freeware	B-License
for	O
academic	O
and	O
noncommercial	O
users	O
registered	O
to	O
HIVE	O
deployment	O
instance	O
2014	O
IMOS	O
Improved	O
Meta-aligner	O
and	O
Minimap2	O
On	O
Spark	B-Language
.	O
</s>
<s>
A	O
long	O
read	O
distributed	O
aligner	O
on	O
Apache	B-Language
Spark	I-Language
platform	O
with	O
linear	O
scalability	O
w.r.t.	O
</s>
<s>
Isaac	O
Fully	O
uses	O
all	O
the	O
computing	O
power	O
available	O
on	O
one	O
server	O
node	O
;	O
thus	O
,	O
it	O
scales	O
well	O
over	O
a	O
broad	O
range	O
of	O
hardware	O
architectures	O
,	O
and	O
alignment	O
performance	O
improves	O
with	O
hardware	O
abilities	O
,	O
GPL	B-License
LAST	O
Uses	O
adaptative	O
seeds	O
and	O
copes	O
more	O
efficiently	O
with	O
repeat-rich	O
sequences	O
(	O
e.g.	O
</s>
<s>
,	O
GPL	B-License
2011	O
MAQ	O
Ungapped	O
alignment	O
that	O
takes	O
into	O
account	O
quality	O
scores	O
for	O
each	O
base	O
.	O
</s>
<s>
,	O
GPL	B-License
mrFAST	O
,	O
mrsFAST	O
Gapped	O
(	O
mrFAST	O
)	O
and	O
ungapped	O
(	O
mrsFAST	O
)	O
alignment	O
software	O
that	O
implements	O
cache	O
obliviousness	O
to	O
minimize	O
main/cache	O
memory	O
transfers	O
.	O
</s>
<s>
,	O
for	O
structural	O
variation	O
,	O
BSD	B-Operating_System
MOM	O
MOM	O
or	O
maximum	O
oligonucleotide	O
mapping	O
is	O
a	O
query	O
matching	O
tool	O
that	O
captures	O
a	O
maximal	O
length	O
match	O
within	O
the	O
short	O
read	O
.	O
</s>
<s>
Aligns	O
reads	O
using	O
a	O
banded	O
Smith-Waterman	B-Algorithm
algorithm	I-Algorithm
seeded	O
by	O
results	O
from	O
a	O
k-mer	O
hashing	O
scheme	O
.	O
</s>
<s>
MPscan	O
Fast	O
aligner	O
based	O
on	O
a	O
filtration	O
strategy	O
(	O
no	O
indexing	O
,	O
use	O
q-grams	O
and	O
Backward	O
Nondeterministic	O
DAWG	B-General_Concept
Matching	O
)	O
2009	O
Novoalign	O
&	O
NovoalignCS	O
Gapped	O
alignment	O
of	O
single	O
end	O
and	O
paired	O
end	O
Illumina	O
GA	O
I	O
&	O
II	O
,	O
ABI	O
Colour	O
space	O
&	O
ION	O
Torrent	O
reads	O
.	O
</s>
<s>
Multi-threading	O
and	O
MPI	O
versions	O
available	O
with	O
paid	O
license	O
,	O
freeware	B-License
single	O
threaded	O
version	O
for	O
academic	O
and	O
noncommercial	O
use	O
NextGENe	O
Developed	O
for	O
use	O
by	O
biologists	O
performing	O
analysis	O
of	O
next	O
generation	O
sequencing	O
data	O
from	O
Roche	O
Genome	O
Sequencer	O
FLX	O
,	O
Illumina	O
GA/HiSeq	O
,	O
Life	O
Technologies	O
Applied	O
BioSystems’	O
SOLiD	O
System	O
,	O
PacBio	O
and	O
Ion	O
Torrent	O
platforms	O
.	O
</s>
<s>
,	O
commercial	B-Application
NextGenMap	O
Flexible	O
and	O
fast	O
read	O
mapping	O
program	O
(	O
twice	O
as	O
fast	O
as	O
BWA	O
)	O
,	O
achieves	O
a	O
mapping	O
sensitivity	O
comparable	O
to	O
Stampy	O
.	O
</s>
<s>
Internally	O
uses	O
a	O
memory	O
efficient	O
index	O
structure	O
(	O
hash	B-Algorithm
table	I-Algorithm
)	O
to	O
store	O
positions	O
of	O
all	O
13-mers	O
present	O
in	O
the	O
reference	O
genome	O
.	O
</s>
<s>
Uses	O
fast	O
SIMD	O
instructions	O
(	O
SSE	B-General_Concept
)	O
to	O
accelerate	O
alignment	O
calculations	O
on	O
CPU	O
.	O
</s>
<s>
If	O
available	O
,	O
alignments	O
are	O
computed	O
on	O
GPU	O
(	O
using	O
OpenCL/CUDA	O
)	O
further	O
reducing	O
runtime	O
20-50	O
%	O
.	O
</s>
<s>
,	O
POSIX	B-Operating_System
Threads	I-Operating_System
,	O
OpenCL/CUDA	O
,	O
SSE	B-General_Concept
2013	O
Omixon	O
Variant	O
Toolkit	O
Includes	O
highly	O
sensitive	O
and	O
highly	O
accurate	O
tools	O
for	O
detecting	O
SNPs	O
and	O
indels	O
.	O
</s>
<s>
,	O
commercial	B-Application
PALMapper	O
Efficiently	O
computes	O
both	O
spliced	O
and	O
unspliced	O
alignments	O
at	O
high	O
accuracy	O
.	O
</s>
<s>
Relying	O
on	O
a	O
machine	O
learning	O
strategy	O
combined	O
with	O
a	O
fast	O
mapping	O
based	O
on	O
a	O
banded	O
Smith-Waterman-like	O
algorithm	O
,	O
it	O
aligns	O
around	O
7	O
million	O
reads	O
per	O
hour	O
on	O
one	O
CPU	O
.	O
</s>
<s>
,	O
GPL	B-License
Partek	O
Flow	O
For	O
use	O
by	O
biologists	O
and	O
bioinformaticians	O
.	O
</s>
<s>
Multiprocessor-core	O
,	O
client-server	O
installation	O
possible	O
,	O
commercial	B-Application
,	O
free	O
trial	O
version	O
PASS	O
Indexes	O
the	O
genome	O
,	O
then	O
extends	O
seeds	O
using	O
pre-computed	O
alignments	O
of	O
words	O
.	O
</s>
<s>
,	O
freeware	B-License
for	O
academic	O
and	O
noncommercial	O
use	O
PerM	O
Indexes	O
the	O
genome	O
with	O
periodic	O
seeds	O
to	O
quickly	O
find	O
alignments	O
with	O
full	O
sensitivity	O
up	O
to	O
four	O
mismatches	O
.	O
</s>
<s>
,	O
GPL	B-License
PRIMEX	O
Indexes	O
the	O
genome	O
with	O
a	O
k-mer	O
lookup	O
table	O
with	O
full	O
sensitivity	O
up	O
to	O
an	O
adjustable	O
number	O
of	O
mismatches	O
.	O
</s>
<s>
,	O
client-server	O
,	O
GPL	B-License
2	O
RazerS	O
No	O
read	O
length	O
limit	O
.	O
</s>
<s>
,	O
LGPL	B-Application
REAL	O
,	O
cREAL	O
REAL	O
is	O
an	O
efficient	O
,	O
accurate	O
,	O
and	O
sensitive	O
tool	O
for	O
aligning	O
short	O
reads	O
obtained	O
from	O
next-generation	O
sequencing	O
.	O
</s>
<s>
,	O
GPL	B-License
RMAP	O
Can	O
map	O
reads	O
with	O
or	O
without	O
error	O
probability	O
information	O
(	O
quality	O
scores	O
)	O
and	O
supports	O
paired-end	O
reads	O
or	O
bisulfite-treated	O
read	O
mapping	O
.	O
</s>
<s>
,	O
GPL	B-License
3rNA	O
A	O
randomized	O
Numerical	O
Aligner	O
for	O
Accurate	O
alignment	O
of	O
NGS	O
reads	O
Multithreading	O
and	O
MPI-enabled	O
,	O
GPL	B-License
3	O
RTG	O
Investigator	O
Extremely	O
fast	O
,	O
tolerant	O
to	O
high	O
indel	O
and	O
substitution	O
counts	O
.	O
</s>
<s>
,	O
for	O
variant	O
calling	O
,	O
freeware	B-License
for	O
individual	O
investigator	O
use	O
Segemehl	O
Can	O
handle	O
insertions	O
,	O
deletions	O
,	O
mismatches	O
;	O
uses	O
enhanced	O
suffix	O
arrays	O
,	O
freeware	B-License
for	O
noncommercial	O
use2009	O
SeqMap	O
Up	O
to	O
5	O
mixed	O
substitutions	O
and	O
insertions-deletions	O
;	O
various	O
tuning	O
options	O
and	O
input-output	O
formats	O
,	O
freeware	B-License
for	O
academic	O
and	O
noncommercial	O
use	O
Shrec	O
Short	O
read	O
error	O
correction	O
with	O
a	O
suffix	B-Architecture
tree	I-Architecture
data	O
structure	O
,	O
Java	B-Language
SHRiMP	O
Indexes	O
the	O
reference	O
genome	O
as	O
of	O
version	O
2	O
.	O
</s>
<s>
,	O
OpenMP	B-Application
,	O
,	O
BSD	B-Operating_System
derivative	O
2009-2011	O
SLIDER	O
Slider	O
is	O
an	O
application	O
for	O
the	O
Illumina	O
Sequence	O
Analyzer	O
output	O
that	O
uses	O
the	O
"	O
probability	O
"	O
files	O
instead	O
of	O
the	O
sequence	O
files	O
as	O
an	O
input	O
for	O
alignment	O
to	O
a	O
reference	O
sequence	O
or	O
a	O
set	O
of	O
reference	O
sequences	O
.	O
</s>
<s>
Speed	O
improvement	O
over	O
BLAT	B-Application
,	O
uses	O
a	O
12	O
letter	O
hash	B-Algorithm
table	I-Algorithm
.	O
</s>
<s>
,	O
SOAP3-dp	O
,	O
POSIX	B-Operating_System
Threads	I-Operating_System
;	O
SOAP3	O
,	O
SOAP3-dp	O
need	O
GPU	O
with	O
CUDA	B-Architecture
support	O
,	O
GPL	B-License
SOCS	O
For	O
ABI	O
SOLiD	O
technologies	O
.	O
</s>
<s>
,	O
GPLSparkBWA	O
Integrates	O
the	O
Burrows	O
–	O
Wheeler	O
Aligner	O
(	O
BWA	O
)	O
on	O
an	O
Apache	B-Language
Spark	I-Language
framework	O
running	O
atop	O
Hadoop	B-Application
.	O
</s>
<s>
,	O
GPL	B-License
32016	O
SSAHA	O
,	O
SSAHA2	O
Fast	O
for	O
a	O
small	O
number	O
of	O
variants	O
,	O
freeware	B-License
for	O
academic	O
and	O
noncommercial	O
use	O
Stampy	O
For	O
Illumina	O
reads	O
.	O
</s>
<s>
,	O
freeware	B-License
for	O
academic	O
and	O
noncommercial	O
use	O
2010	O
SToRM	O
For	O
Illumina	O
or	O
ABI	O
SOLiD	O
reads	O
,	O
with	O
SAM	B-Application
native	O
output	O
.	O
</s>
<s>
Uses	O
spaced	O
seeds	O
(	O
single	O
hit	O
)	O
and	O
a	O
very	O
fast	O
SSE-SSE2-AVX2-AVX-512	O
banded	O
alignment	O
filter	O
.	O
</s>
<s>
,	O
OpenMP	B-Application
2010	O
Subread	O
,	O
Subjunc	O
Superfast	O
and	O
accurate	O
read	O
aligners	O
.	O
</s>
<s>
,	O
GPL	B-License
3	O
Taipan	O
De-novo	O
assembler	O
for	O
Illumina	O
reads	O
,	O
freeware	B-License
for	O
academic	O
and	O
noncommercial	O
use	O
UGENE	B-Language
Visual	O
interface	O
both	O
for	O
Bowtie	B-Application
and	O
BWA	O
,	O
and	O
an	O
embedded	O
aligner	O
,	O
GPL	B-License
VelociMapper	O
FPGA-accelerated	O
reference	O
sequence	B-Algorithm
alignment	I-Algorithm
mapping	O
tool	O
from	O
TimeLogic	B-Application
.	O
</s>
<s>
Faster	O
than	O
Burrows	O
–	O
Wheeler	O
transform-based	O
algorithms	O
like	O
BWA	O
and	O
Bowtie	B-Application
.	O
</s>
<s>
Produces	O
sensitive	O
Smith	B-Algorithm
–	I-Algorithm
Waterman	I-Algorithm
gapped	O
alignments	O
.	O
</s>
<s>
,	O
commercial	B-Application
XpressAlign	O
FPGA	O
based	O
sliding	O
window	O
short	O
read	O
aligner	O
which	O
exploits	O
the	O
embarrassingly	O
parallel	O
property	O
of	O
short	O
read	O
alignment	O
.	O
</s>
<s>
,	O
freeware	B-License
for	O
academic	O
and	O
noncommercial	O
use	O
ZOOM	O
100%	O
sensitivity	O
for	O
a	O
reads	O
between	O
15	O
and	O
240	O
bp	O
with	O
practical	O
mismatches	O
.	O
</s>
