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{{
This '''list of sequence alignment software''' is a compilation of software tools and web portals used in pairwise [[sequence alignment]] and [[multiple sequence alignment]]. See [[structural alignment software]] for [[structural alignment]] of proteins.
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! Year
|-
| [[BLAST (biotechnology)|BLAST]]
| Local search with fast k-tuple heuristic (Basic Local Alignment Search Tool) || Both ||[[Stephen Altschul|Altschul SF]], [[Warren Gish|Gish W]], [[Webb Miller|Miller W]], [[Eugene Myers|Myers EW]], [[David J. Lipman|Lipman DJ]]<ref>{{Cite journal|author=Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ |title=Basic local alignment search tool |journal=Journal of Molecular Biology |volume=215 |issue=3 |pages=403–10 |date=October 1990 |pmid=2231712 |doi=10.1016/S0022-2836(05)80360-2|last2=Gish |last3=Miller |last4=Myers |last5=Lipman|s2cid=14441902 }}</ref> || 1990
|-
| [[HPC-BLAST]]
| NCBI compliant multinode and multicore BLAST wrapper. Distributed with the latest version of BLAST, this wrapper facilitates parallelization of the algorithm on modern hybrid architectures with many nodes and many cores within each node.
|-
| [[CS-BLAST]]
| Sequence-context specific BLAST, more sensitive than BLAST, FASTA, and SSEARCH. Position-specific iterative version CSI-BLAST more sensitive than PSI-BLAST || Protein || Angermueller C, Biegert A, Soeding J<ref>{{Cite journal |last1= Angermüller |first1= C. |last2= Biegert |first2= A. |last3= Söding |first3= J. |title= Discriminative modelling of context-specific amino acid substitution probabilities |journal= Bioinformatics |volume= 28 |issue= 24 |pages= 3240–7|date=Dec 2012 |doi= 10.1093/bioinformatics/bts622 |pmid=23080114|doi-access= free |hdl= 11858/00-001M-0000-0015-8D22-F |hdl-access= free }}</ref>
|| 2013
|-
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|-
| [[HH-suite]]
| Pairwise comparison of profile Hidden Markov models; very sensitive || Protein || Söding J<ref>{{Cite journal|author=Söding J |title=Protein homology detection by HMM-HMM comparison |journal=Bioinformatics |volume=21 |issue=7 |pages=951–60 |date=April 2005 |pmid=15531603 |doi=10.1093/bioinformatics/bti125|doi-access=free |hdl=11858/00-001M-0000-0017-EC7A-F |hdl-access=free }}</ref><ref>{{Cite journal|last1=Remmert|first1=Michael|last2=Biegert|first2=Andreas|last3=Hauser|first3=Andreas|last4=Söding|first4=Johannes|date=2011-12-25|title=HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment|journal=Nature Methods|volume=9|issue=2|pages=173–175|doi=10.1038/nmeth.1818|issn=1548-7105|pmid=22198341|hdl=11858/00-001M-0000-0015-8D56-A|s2cid=205420247|hdl-access=free}}</ref> ||2005/2012
|-
| IDF
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|-
| MMseqs2
| Software suite to search and cluster huge sequence sets. Similar sensitivity to BLAST and PSI-BLAST but orders of magnitude faster || Protein || Steinegger M, Mirdita M, Galiez C, Söding J<ref>{{Cite journal|last1=Steinegger|first1=Martin|last2=Soeding|first2=Johannes|date=2017-10-16|journal=Nature Biotechnology|volume=35|issue=11|pages=1026–1028|title=MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets|url=https://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3988.html|doi=10.1038/nbt.3988|pmid=29035372|hdl=11858/00-001M-0000-002E-1967-3|s2cid=402352|hdl-access=free|url-access=subscription}}</ref> || 2017
|-
| USEARCH
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|OpenCL Smith-Waterman on Altera's FPGA for Large Protein Databases
|Protein
|Rucci E, García C, Botella G, De Giusti A, Naiouf M, Prieto-Matías M<ref>{{Cite journal|last1=Rucci|first1=Enzo|last2=Garcia|first2=Carlos|last3=Botella|first3=Guillermo|last4=Giusti|first4=Armando E. De|last5=Naiouf|first5=Marcelo|last6=Prieto-Matias|first6=Manuel|date=2016-06-30|title=OSWALD: OpenCL Smith–Waterman on Altera's FPGA for Large Protein Databases|url=http://hpc.sagepub.com/content/early/2016/06/30/1094342016654215|journal=International Journal of High Performance Computing Applications|volume=32|issue=3|pages=337–350|doi=10.1177/1094342016654215|s2cid=212680914|issn=1094-3420|hdl=11336/48798|hdl-access=free}}</ref>
|2016
|-
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| PSI-Search
| Combining the Smith-Waterman search algorithm with the [[PSI-BLAST]] profile construction strategy to find distantly related protein sequences, and preventing homologous over-extension errors. || Protein || Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR<ref>{{Cite journal|author=Li W |title=PSI-Search: iterative HOE-reduced profile SSEARCH searching |journal=Bioinformatics |volume=28 |issue=12 |pages=1650–1651 |date=June 2012 |pmid=22539666 |pmc=3371869 |doi=10.1093/bioinformatics/bts240 |name-list-style=vanc|author2= McWilliam H|author3=Goujon M|display-authors=3|last4=Cowley|first4=A|last5=Lopez|first5=R|last6=Pearson|first6=WR}}</ref> || 2012
|-▼
|R&R
|Retrieve and Relate (R&R) is a high performance yet sensitive multi-database search engine, capable of searching in parallel through DNA,RNA and Protein sequences.
|Both
|▼
|2019
|-
| ScalaBLAST
| Highly parallel Scalable BLAST || Both || Oehmen et al.<ref>{{cite journal
|last1=Oehmen |first1=C.|last2= Nieplocha |first2=J. |title=ScalaBLAST: A scalable implementation of BLAST for high-performance data-intensive bioinformatics analysis|journal=IEEE Transactions on Parallel
|doi=10.1109/TPDS.2006.112|s2cid=11122366|url=https://zenodo.org/record/1232261 }}</ref>||2011
|-
Line 101 ⟶ 107:
|-
| SWIMM
| Smith-Waterman implementation for Intel Multicore and Manycore architectures || Protein || Rucci E, García C, Botella G, De Giusti A, Naiouf M and Prieto-Matías M<ref>{{Cite journal|last1=Rucci|first1=Enzo|last2=García|first2=Carlos|last3=Botella|first3=Guillermo|last4=De Giusti|first4=Armando|last5=Naiouf|first5=Marcelo|last6=Prieto-Matías|first6=Manuel|date=2015-12-25|title=An energy-aware performance analysis of SWIMM: Smith–Waterman implementation on Intel's Multicore and Manycore architectures|journal=Concurrency and Computation: Practice and Experience|volume=27|issue=18|pages=5517–5537|doi=10.1002/cpe.3598|s2cid=42945406|issn=1532-0634|url=http://sedici.unlp.edu.ar/handle/10915/82869|hdl=11336/53930|hdl-access=free}}</ref>|| 2015
|-
| SWIMM2.0
Line 110 ⟶ 116:
|}
<small><nowiki>*</nowiki>'''Sequence type:''' protein or nucleotide</small>
==Pairwise alignment==
Line 139 ⟶ 144:
| BLASTZ, LASTZ
| Seeded pattern-matching || Nucleotide || Local || Schwartz ''et al.''<ref>{{Cite journal| author=Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W| title=Human-mouse alignments with BLASTZ| journal=Genome Research |volume=13 |issue=1 |date=2003 |pages=103–107 |pmid=12529312 | pmc=430961| doi=10.1101/gr.809403| last2=Kent| last3=Smit| last4=Zhang| last5=Baertsch| last6=Hardison| last7=Haussler| last8=Miller}}</ref><ref>{{Cite thesis| author=Harris R S | year=2007| title=Improved pairwise alignment of genomic DNA}}</ref> || 2004,2009
|-▼
| [[CodonCode Aligner]]
| Fast pairwise and multi-sequence alignments with multiple algorithms. || Nucleotide || Both || CodonCode Corporation || 2003-2025
|-
| CUDAlign
| DNA sequence alignment of unrestricted size in single or multiple GPUs
|| Nucleotide || Local, SemiGlobal, Global || E. Sandes<ref>{{Cite journal|author=Sandes, Edans F. de O. |author2=de Melo, Alba Cristina M.A.|title=Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences Using GPU |journal=IEEE Transactions on Parallel and Distributed Systems|volume=24 |issue=5 | pages=1009–1021 |date=May 2013 |doi=10.1109/TPDS.2012.194}}</ref><ref>{{Cite conference|author=Sandes, Edans F. de O. |author2=Miranda, G. |author3=De Melo, A.C.M.A. |author4=Martorell, X. |author5=Ayguade, E.|title=CUDAlign 3.0: Parallel Biological Sequence Comparison in Large GPU Clusters |conference=Cluster, Cloud and Grid Computing (CCGrid), 2014 14th IEEE/ACM International Symposium on |page=160 |date=May 2014 |doi=10.1109/CCGrid.2014.18|hdl=2117/24766 |hdl-access=free }}</ref><ref>{{Cite conference|author=Sandes, Edans F. de O. |author2=Miranda, G. |author3=De Melo, A.C.M.A. |author4=Martorell, X. |author5=Ayguade, E.|title=Fine-grain Parallel Megabase Sequence Comparison with Multiple Heterogeneous GPUs |conference=Proceedings of the 19th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming |pages=383–384 |date=August 2014 |doi=10.1145/2555243.2555280|hdl=2117/23094 |hdl-access=free }}</ref> || 2011-2015
|-
| DNADot
| Web-based dot-plot tool || Nucleotide || Global || R. Bowen || 1998
▲|-
| MegAlign Pro (Lasergene Molecular Biology)▼
| Software to align DNA, RNA, protein, or DNA + protein sequences via pairwise and multiple sequence alignment algorithms including MUSCLE, Mauve, MAFFT, Clustal Omega, Jotun Hein, Wilbur-Lipman, Martinez Needleman-Wunsch, Lipman-Pearson and Dotplot analysis. || Both || Both ||[[DNASTAR]] ||1993-2016▼
|-
| DOTLET
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| NW-align
| Standard Needleman-Wunsch dynamic programming algorithm || Protein || Global || Y Zhang || 2012
▲|-
|-
| matcher
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| MCALIGN2
| explicit models of indel evolution || DNA || Global || J. Wang ''et al.'' || 2006
|-▼
▲| MegAlign Pro (Lasergene Molecular Biology)
▲| Software to align DNA, RNA, protein, or DNA + protein sequences via pairwise and multiple sequence alignment algorithms including MUSCLE, Mauve, MAFFT, Clustal Omega, Jotun Hein, Wilbur-Lipman, Martinez Needleman-Wunsch, Lipman-Pearson and Dotplot analysis. || Both || Both ||[[DNASTAR]] ||1993-2016
|-
| MUMmer
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|-
| Path
| [[Smith-Waterman]] on [[protein]] back-[[translation (genetics)|translation]] [[Chart|graph]] (detects [[frameshift]]s at protein level) || Protein || Local || M. Gîrdea ''et al.''<ref>{{Cite journal |last1=Girdea |first1=M |last2=Noe |first2=L |last3=Kucherov |first3=G |title=Back-translation for discovering distant protein homologies in the presence of frameshift mutations |journal=Algorithms for Molecular Biology |volume=5 |issue=6 |page=6 |date=January 2010 |pmid=20047662 |pmc=2821327 |doi=10.1186/1748-7188-5-6 |doi-access=free }}</ref> || 2009
|-
| [[PatternHunter]]
Line 252 ⟶ 257:
| SWIFOLD
| Smith-Waterman Acceleration on Intel's FPGA with OpenCL for Long DNA Sequences
|| Nucleotide || Local || E. Rucci<ref>{{Cite journal|author=Rucci, Enzo |author2=Garcia, Carlos|author3=Botella, Guillermo|author4=Naiouf, Marcelo|author5=De Giusti,Armando|author6=Prieto-Matias, Manuel|title=SWIFOLD: Smith-Waterman implementation on FPGA with OpenCL for long DNA sequences |journal=BMC Systems Biology|volume=12 | doi=10.1186/s12918-018-0614-6|doi-access=free |year=2018|issue=Suppl 5|page=96|pmid=30458766|pmc=6245597}}</ref><ref>{{Cite conference|author=Rucci, Enzo |author2=Garcia, Carlos|author3=Botella, Guillermo|author4=Naiouf, Marcelo|author5=De Giusti,Armando|author6=Prieto-Matias, Manuel|title=Accelerating Smith-Waterman Alignment of Long DNA Sequences with OpenCL on FPGA |conference=5th International Work-Conference on Bioinformatics and Biomedical Engineering |
|-
| SWIFT suit
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| [[AMAP]]
| Sequence annealing || Both || Global || A. Schwartz and [[Lior Pachter|L. Pachter]] || 2006 ||
▲|-
|-
| [[BAli-Phy]]
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| Iterative alignment || Both || Local (preferred) || M. Brudno and B. Morgenstern || 2003 ||
|-
| [[Clustal]]
| Progressive alignment || Both || Local or global || Thompson ''et al.'' || 1994 || {{free}}, [[GNU Lesser General Public License|LGPL]]
|-
| [[CodonCode Aligner]]
| Multi-alignment;
|-
| [[Compass]]
Line 336 ⟶ 338:
| [[DNADynamo]]
| linked DNA to Protein [[Multiple sequence alignment|multiple alignment]] with [[MUSCLE (alignment software)|MUSCLE]], [[Clustal]] and Smith-Waterman|| Both || Local or global || DNADynamo || 2004 (newest version 2017) ||
|-▼
| MegAlign Pro (Lasergene Molecular Biology)▼
| Software to align DNA, RNA, protein, or DNA + protein sequences via pairwise and multiple sequence alignment algorithms including MUSCLE, Mauve, MAFFT, Clustal Omega, Jotun Hein, Wilbur-Lipman, Martinez Needleman-Wunsch, Lipman-Pearson and Dotplot analysis. || Both || Local or global ||[[DNASTAR]] || 1993-2016 ||▼
|-
| EDNA
Line 349 ⟶ 348:
|Deorowicz et al.
|2016
|{{free}}, [[GNU General Public License|GPL]] 3
▲|
|-
| [[Fast Statistical Alignment|FSA]]
Line 356 ⟶ 355:
| [[Geneious]]
| Progressive-Iterative alignment; ClustalW plugin || Both || Local or global || A.J. Drummond ''et al.'' || 2005 (latest version 2017) ||
▲|-
| GUIDANCE
| Quality control and filtering of multiple sequence alignments || Both || Local or global || O. Penn ''et al.'' || 2010 (latest version 2015) ||
|-
| Kalign
| Progressive alignment || Both || Global || T. Lassmann || 2005 ||
|-
|MACSE
|Progressive-iterative alignment. Multiple alignment of coding sequences accounting for frameshifts and stop codons.
|Nucleotides
|Global
|V. Ranwez ''et al.''
|2011 (latest version, v2.07 2023)
|
|-
| [[MAFFT]]
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| [[MAVID]]
| Progressive alignment || Both || Global || N. Bray and [[Lior Pachter|L. Pachter]] || 2004 ||
|-
▲| MegAlign Pro (Lasergene Molecular Biology)
▲| Software to align DNA, RNA, protein, or DNA + protein sequences via pairwise and multiple sequence alignment algorithms including MUSCLE, Mauve, MAFFT, Clustal Omega, Jotun Hein, Wilbur-Lipman, Martinez Needleman-Wunsch, Lipman-Pearson and Dotplot analysis. || Both || Local or global ||[[DNASTAR]] || 1993-
|-
| MSA
Line 382 ⟶ 395:
|-
| [[MUSCLE (alignment software)|MUSCLE]]
| Progressive-iterative alignment (v3), Probabilistic/consistency (v5) || Both || Local or global || R. Edgar || 2004 || Public ___domain
|-
| Opal
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|-
| Shuffle-LAGAN
| Pairwise
|-
| SIBsim4, [[Sim4]]
Line 641 ⟶ 654:
| {{yes}}
| {{free}}, [[BSD licenses|BSD]]
|<ref name="WiltonEtAl2015">{{cite journal|last1=Wilton|first1=Richard|last2=Budavari|first2=Tamas|last3=Langmead|first3=Ben|last4=Wheelan|first4=Sarah J.|last5=Salzberg|first5=Steven L.|last6=Szalay|first6=Alexander S.|title=Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space|journal=PeerJ|volume=3|pages=e808|year=2015|doi=10.7717/peerj.808|pmid=25780763|pmc=4358639 |doi-access=free }}</ref>
| 2015
|-
| BarraCUDA
| A GPGPU accelerated [[
| {{yes}}
| {{no}}
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|-
| BBMap
| Uses a short kmers to rapidly index genome; no size or scaffold count limit. Higher sensitivity and specificity than
| {{yes}}
| {{yes}}
Line 671 ⟶ 684:
| {{yes}}, [[POSIX Threads]]
| {{free}}, [[GNU General Public License|GPL]]
|<ref name="HomerMerrimanNelson2009">{{cite journal|last1=Homer|first1=Nils|last2=Merriman|first2=Barry|last3=Nelson|first3=Stanley F.|title=BFAST: An Alignment Tool for Large Scale Genome Resequencing|journal=PLOS ONE|volume=4|issue=11|year=2009|pages=e7767|pmid=19907642|pmc=2770639|doi=10.1371/journal.pone.0007767|bibcode=2009PLoSO...4.7767H|doi-access=free}}</ref>
| 2009
|-
| BigBWA
| Runs the [[
| {{yes}}
| {{partial|Low quality bases trimming}}
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|-
| [[Bowtie (sequence analysis)|Bowtie]]
| Uses a [[
| {{yes}}
| {{yes}}
Line 712 ⟶ 725:
| {{yes}}, [[POSIX Threads]]
| {{free}}, [[Artistic License|Artistic]]
|<ref name="LangmeadTrapnell2009">{{cite journal|last1=Langmead|first1=Ben|last2=Trapnell|first2=Cole|last3=Pop|first3=Mihai|last4=Salzberg|first4=Steven L|title=Ultrafast and memory-efficient alignment of short DNA sequences to the human genome|journal=Genome Biology|volume=10|issue=3|year=2009|pages=R25|issn=1465-6906|doi=10.1186/gb-2009-10-3-r25|pmid=19261174|pmc=2690996 |doi-access=free }}</ref>
|2009
|-
| BWA
| Uses a [[
| {{yes}}
| {{partial|Low quality bases trimming}}
Line 722 ⟶ 735:
| {{yes}}
| {{free}}, [[GNU General Public License|GPL]]
|<ref name="LiDurbin2009">{{cite journal|last1=Li|first1=H.|last2=Durbin|first2=R.|title=Fast and accurate short read alignment with
| 2009
|-
Line 732 ⟶ 745:
| {{yes}}
| {{free}}, [[GNU General Public License|GPL]]
|<ref name="KerpedjievFrellsen2014">{{cite journal|last1=Kerpedjiev|first1=Peter|last2=Frellsen|first2=Jes|last3=Lindgreen|first3=Stinus|last4=Krogh|first4=Anders|title=Adaptable probabilistic mapping of short reads using position specific scoring matrices|journal=BMC Bioinformatics|volume=15|issue=1|year=2014|page=100|issn=1471-2105|doi=10.1186/1471-2105-15-100|pmid=24717095|pmc=4021105 |doi-access=free }}</ref>
| 2014
|-
Line 752 ⟶ 765:
| {{yes}}, [[Hadoop]] [[MapReduce]]
| {{free}}, [[Artistic License|Artistic]]
|
|
|-
| CodonCode Aligner
| Fast assembly, accurate consensus sequences with support for quality scores. Compare Contigs, Phred, Phrap, and Bowtie support. Build separate contigs for hundreds of different clones or a single contig with thousands of sequences.
|{{yes}}
|{{yes}}
|{{yes}}
|{{yes}}
|{{proprietary}}, [[Commercial software|commercial]]
|
|
Line 766 ⟶ 789:
|-
|CUSHAW
| A CUDA compatible short read aligner to large genomes based on
| {{yes}}
| {{yes}}
Line 772 ⟶ 795:
| {{yes}} (GPU enabled)
| {{free}}, [[GNU General Public License|GPL]]
|<ref name="LiuSchmidt2012a">{{cite journal|last1=Liu|first1=Y.|last2=Schmidt|first2=B.|last3=Maskell|first3=D. L.|title=CUSHAW: a CUDA compatible short read aligner to large genomes based on the
|2012
|-
Line 912 ⟶ 935:
| {{yes}}
| {{proprietary}}, [[freeware]] for academic and noncommercial users registered to HIVE deployment instance
|<ref name="VSimonyan2014">{{cite journal|last1=Santana-Quintero|first1=Luis|last2=Dingerdissen|first2=Hayley|last3=Thierry-Mieg|first3=Jean|last4=Mazumder|first4=Raja|last5=Simonyan|first5=Vahan|title=HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis|journal=PLOS ONE|year=2014|pages=1754–1760|doi=10.1371/journal.pone.0099033|pmid=24918764|volume=9|issue=6|pmc=4053384|bibcode=2014PLoSO...999033S|doi-access=free}}</ref>
| 2014
|-
Line 993 ⟶ 1,016:
|
|
| <ref name="RivalsEtAl2009">{{cite book|last1=Rivals|first1=Eric|last2=Salmela|first2=Leena|last3=Kiiskinen|first3=Petteri|last4=Kalsi|first4=Petri|last5=Tarhio|first5=Jorma|title=
| 2009
|-
Line 1,153 ⟶ 1,176:
| {{yes}}
| {{proprietary}}, [[freeware]] for noncommercial use
|<ref name="SearlsHoffmann2009">{{cite journal|last1=Searls|first1=David B.|last2=Hoffmann|first2=Steve|last3=Otto|first3=Christian|last4=Kurtz|first4=Stefan|last5=Sharma|first5=Cynthia M.|last6=Khaitovich|first6=Philipp|last7=Vogel|first7=Jörg|last8=Stadler|first8=Peter F.|last9=Hackermüller|first9=Jörg|title=Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures|journal=PLOS Computational Biology|volume=5|issue=9|year=2009|pages=e1000502|issn=1553-7358|doi=10.1371/journal.pcbi.1000502|pmid=19750212|pmc=2730575|bibcode=2009PLSCB...5E0502H |doi-access=free }}</ref>
|2009
|-
Line 1,182 ⟶ 1,205:
| {{yes}}
| {{yes}}, [[OpenMP]]
| {{free}}, [[BSD licenses
| {{free}}, [[BSD licenses|BSD]]]] derivative |
<ref name="RumbleLacrouteDalcaFiumeSidowBrudno2009">{{cite journal|last1=Rumble|first1=Stephen M.|last2=Lacroute|first2=Phil|last3=Dalca|first3=Adrian V.|last4=Fiume|first4=Marc|last5=Sidow|first5=Arend|last6=Brudno|first6=Michael|title=SHRiMP: Accurate Mapping of Short Color-space Reads|journal=PLOS Computational Biology
|volume=5|issue=5|year=2009|pages=e1000386|pmid=19461883|pmc=2678294|doi=10.1371/journal.pcbi.1000386|bibcode=2009PLSCB...5E0386R |doi-access=free }}</ref>
<ref name="DavidDzambaListerIlieBrudno2011">{{cite journal|last1=David|first1=Matei|last2=Dzamba|first2=Misko|last3=Lister|first3=Dan|last4= Ilie|first4=Lucian|last5=Brudno|first5=Michael|title=SHRiMP2: Sensitive yet Practical Short Read Mapping|journal=Bioinformatics|volume=27|issue=7|year=2011|pages=1011–1012|pmid=21278192|doi=10.1093/bioinformatics/btr046|doi-access=free}}</ref>
| 2009-2011
Line 1,198 ⟶ 1,222:
|<ref name="MalhisButterfieldEsterJones2009">{{cite journal|last1=Malhis|first1=Nawar|last2=Butterfield|first2=Yaron S. N.|last3=Ester|first3=Martin|last4=Jones|first4=Steven J. M.|title=Slider – Maximum use of probability information for alignment of short sequence reads and SNP detection|journal=Bioinformatics
|volume=25|issue=1|year=2009|pages=6–13|pmid=18974170|pmc=2638935|doi=10.1093/bioinformatics/btn565}}</ref><ref name="MalhisJones2010">{{cite journal|last1=Malhis|first1=Nawar|last2=Jones|first2=Steven J. M.|title=High Quality SNP Calling Using Illumina Data at Shallow Coverage|journal=Bioinformatics
|volume=26|issue=8|year=2010|pages=1029–1035|pmid=20190250|doi=10.1093/bioinformatics/btq092|doi-access=
| 2009-2010
|-
Line 1,208 ⟶ 1,232:
| {{yes}}, [[POSIX Threads]]; SOAP3, SOAP3-dp need GPU with [[CUDA]] support
| {{free}}, [[GNU General Public License|GPL]]
|<ref name="LiLi2008">{{cite journal|last1=Li|first1=R.|last2=Li|first2=Y.|last3=Kristiansen|first3=K.|last4=Wang|first4=J.|title=SOAP: short oligonucleotide alignment program|journal=Bioinformatics|volume=24|issue=5|year=2008|pages=713–714|issn=1367-4803|doi=10.1093/bioinformatics/btn025|pmid=18227114|doi-access=free}}</ref><ref name="LiYu2009">{{cite journal|last1=Li|first1=R.|last2=Yu|first2=C.|last3=Li|first3=Y.|last4=Lam|first4=T.-W.|last5=Yiu|first5=S.-M.|last6=Kristiansen|first6=K.|last7=Wang|first7=J.|title=SOAP2: an improved ultrafast tool for short read alignment|journal=Bioinformatics|volume=25|issue=15|year=2009|pages=1966–1967|issn=1367-4803|doi=10.1093/bioinformatics/btp336|pmid=19497933|doi-access=
|
|-
Line 1,222 ⟶ 1,246:
|-
|SparkBWA
| Integrates the [[
| {{yes}}
| {{partial|Low quality bases trimming}}
Line 1,228 ⟶ 1,252:
| {{yes}}
| {{free}}, [[GNU General Public License|GPL]] 3
|<ref>{{Cite journal|last1=Abuín|first1=José M.|last2=Pichel|first2=Juan C.|last3=Pena|first3=Tomás F.|last4=Amigo|first4=Jorge|date=2016-05-16|title=SparkBWA: Speeding Up the Alignment of High-Throughput DNA Sequencing Data|journal=PLOS ONE|volume=11|issue=5|pages=e0155461|doi=10.1371/journal.pone.0155461|issn=1932-6203|pmid=27182962|pmc=4868289|bibcode=2016PLoSO..1155461A|doi-access=free}}</ref>
|2016
|-
Line 1,258 ⟶ 1,282:
| {{yes}}, [[OpenMP]]
| {{free}}
|<ref name="NoeGirdeaKucherov2010">{{cite journal|last1=Noe|first1=L.|last2=Girdea|first2=M.|last3=Kucherov|first3=G.|title=Designing efficient spaced seeds for SOLiD read mapping|journal=Advances in Bioinformatics|volume=2010|year=2010|page=708501|pmid=20936175|pmc=2945724|doi=10.1155/2010/708501|doi-access=free}}</ref>
|2010
|-
Line 1,292 ⟶ 1,316:
|-
| VelociMapper
| FPGA-accelerated reference sequence alignment mapping tool from [[TimeLogic]]. Faster than [[
| {{yes}}
| {{yes}}
Line 1,312 ⟶ 1,336:
|-
| ZOOM
| 100% sensitivity for a reads between 15
|
|
Line 1,328 ⟶ 1,352:
{{Reflist}}
[[Category:Database-related lists|Seq]]
[[Category:
[[Category:Lists of bioinformatics software|Sequence alignment software]]
| |||