List of sequence alignment software: Difference between revisions

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{{shortShort description|Wikipedia list articlenone}}

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. <ref>HPC-BLAST code repository https://github.com/UTennessee-JICS/HPC-BLAST</ref>|| Protein || [[Chad Burdyshaw|Burdyshaw CE]], [[Shane Sawyer|Sawyer S]], [[Mitch Horton| Horton MD]], [[Glenn Brook| Brook RG]], [[Bhanu Rekapalli| Rekapalli B]] || 2017

|-

| [[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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|-

| DIAMOND

| BLASTX and BLASTP aligner based on double indexing || Protein || Buchfink B, Xie, C and, Huson DH, Reuter K, Drost HG <ref>{{Cite journal |author=Buchfink, Xie and Huson |title=Fast and sensitive protein alignment using DIAMOND |journal=Nature Methods |volume=12 |issue=1 |pages=59–60 |date= 2015 |doi=10.1038/nmeth.3176|pmid=25402007 |s2cid=5346781 }}</ref><ref>{{Cite journal |author=B Buchfink, K Reuter and HG Drost |title=Sensitive protein alignments at tree-of-life scale using DIAMOND |journal=Nature Methods |volume=18 |pages=366–368 |date= 2021 |issue=4 |doi=10.1038/s41592-021-01101-x|pmid=33828273 |pmc=8026399 |doi-access=free }}</ref>

|| 2015/2021

|-

| [[FASTA]]

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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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|-

| LAMBDA

| High performance local aligner compatible to BLAST, but much faster; supports SAM/BAM || Protein || Hannes Hauswedell, Jochen Singer, Knut Reinert<ref>{{Cite journal|last1=Hauswedell|first1=Hannes|last2=Singer|first2=Jochen|last3=Reinert|first3=Knut|date=2014-09-01|journal=Bioinformatics|volume=30 |issue=17 |pages=349–355| title=Lambda: the local aligner for massive biological data|url=http://bioinformatics.oxfordjournals.org/content/30/17/i349.abstract |pmid=25161219|pmc=4147892 |name-list-style=vanc|doi=10.1093/bioinformatics/btu439}}</ref>|| 2014

|-

|-

| 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 &and Distributed Systems |volume=17 |issue=8 |pages=740–749 |date=August 2006|

|doi=10.1109/TPDS.2006.112|s2cid=11122366|url=https://zenodo.org/record/1232261 }}</ref>||2011

|-

| Sequilab

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|-

| 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

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| 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

|-

| [[DNASTAR]] Lasergene Molecular Biology Suite

| 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

|-

| mAlign

| modelling alignment; models the information content of the sequences || Nucleotide || Both || D. Powell, L. Allison and T. I. Dix || 2004

|-

| matcher

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| MCALIGN2

| explicit models of indel evolution || DNA || Global || J. Wang ''et al.'' || 2006

|-

| [[DNASTAR]]MegAlign Pro (Lasergene Molecular Biology Suite)

| 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]]

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| 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 |pagepages=500-511500–511 |doi=10.1007/978-3-319-56154-7_45}}</ref> || 2017-2018

|-

| SWIFT suit

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| [[AMAP]]

| Sequence annealing || Both || Global || A. Schwartz and [[Lior Pachter|L. Pachter]] || 2006 ||

|-

| anon.

| fast, optimal alignment of three sequences using linear gap costs || Nucleotides || Global || D. Powell, L. Allison and T. I. Dix || 2000 ||

|-

| [[BAli-Phy]]

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| Iterative alignment || Both || Local (preferred) || M. Brudno and B. Morgenstern || 2003 ||

|-

| [[Clustal]]W

| Progressive alignment || Both || Local or global || Thompson ''et al.'' || 1994 || {{free}}, [[GNU Lesser General Public License|LGPL]]

|-

| [[CodonCode Aligner]]

| Multi-alignment; ClustalWMuscle, Clustal & Phrap support || Nucleotides || Local or global || P. Richterich ''et al.'' || 2003 (latest version 20092024) ||

|-

| [[Compass]]

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| [[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) ||

|-

| [[DNASTAR]] Lasergene Molecular Biology Suite

| 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

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|Deorowicz et al.

|2016

|{{free}}, [[GNU General Public License|GPL]] 3

|

|-

| [[Fast Statistical Alignment|FSA]]

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| [[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 ||

|-

| [[DNASTAR]]MegAlign Pro (Lasergene Molecular Biology Suite)

| 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]] || 1993-20162023 ||

|-

| MSA

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|-

| [[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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! Sequence type*

|-

| EAGLE <ref name="Pratas2020">{{cite journal|last1=Pratas|first1=Diogo|last2=Silva|first2=Jorge|title=Persistent minimal sequences of SARS-CoV-2|journal=Bioinformatics|year=2020|volume=36|issue=21|pages=5129–5132|doi=10.1093/bioinformatics/btaa686|pmid=32730589|pmc=7559010|doi-access=free}}</ref>

| An ultra-fast tool to find relative absent words in genomic data

| Nucleotide

Line 511 ⟶ 525:

|-

| Shuffle-LAGAN

| Pairwise glocalglobal alignment of completed genome regions || Nucleotide

|-

| SIBsim4, [[Sim4]]

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| {{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 [[Burrows-WheelerBurrows–Wheeler transform]] (FM-index) short read alignment program based on BWA, supports alignment of indels with gap openings and extensions.

| {{yes}}

| {{no}}

Line 654 ⟶ 668:

|-

| BBMap

| Uses a short kmers to rapidly index genome; no size or scaffold count limit. Higher sensitivity and specificity than Burrows-WheelerBurrows–Wheeler aligners, with similar or greater speed. Performs affine-transform-optimized global alignment, which is slower but more accurate than Smith-Waterman. Handles Illumina, 454, PacBio, Sanger, and Ion Torrent data. Splice-aware; capable of processing long indels and RNA-seq. Pure Java; runs on any platform. Used by the [[Joint Genome Institute]].

| {{yes}}

| {{yes}}

Line 670 ⟶ 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 [[Burrows-WheelerBurrows–Wheeler Aligner]]-BWA on a [[Hadoop]] cluster. It supports the algorithms BWA-MEM, BWA-ALN, and BWA-SW, working with paired and single reads. It implies an important reduction in the computational time when running in a Hadoop cluster, adding scalability and fault-tolerance.

| {{yes}}

| {{partial|Low quality bases trimming}}

Line 705 ⟶ 719:

|-

| [[Bowtie (sequence analysis)|Bowtie]]

| Uses a [[Burrows-WheelerBurrows–Wheeler transform]] to create a permanent, reusable index of the genome; 1.3 GB memory footprint for human genome. Aligns more than 25 million Illumina reads in 1 CPU hour. Supports Maq-like and SOAP-like alignment policies

| {{yes}}

| {{yes}}

Line 711 ⟶ 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 [[Burrows-WheelerBurrows–Wheeler transform]] to create an index of the genome. It's a bit slower than Bowtie but allows indels in alignment.

| {{yes}}

| {{partial|Low quality bases trimming}}

Line 721 ⟶ 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 Burrows-WheelerBurrows–Wheeler transform|journal=Bioinformatics|volume=25|issue=14|year=2009|pages=1754–1760|issn=1367-4803|doi=10.1093/bioinformatics/btp324|pmid=19451168|pmc=2705234}}</ref>

| 2009

|-

Line 731 ⟶ 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 751 ⟶ 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 765 ⟶ 789:

|-

|CUSHAW

| A CUDA compatible short read aligner to large genomes based on Burrows-WheelerBurrows–Wheeler transform

| {{yes}}

| {{yes}}

Line 771 ⟶ 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 Burrows-WheelerBurrows–Wheeler transform|journal=Bioinformatics|volume=28|issue=14|year=2012|pages=1830–1837|issn=1367-4803|doi=10.1093/bioinformatics/bts276|pmid=22576173|doi-access=free}}</ref>

|2012

|-

Line 850 ⟶ 874:

| {{yes}}

| {{yes}}

| {{free}}, [[GNU General Public License|GPL]]3

| {{Free software; under the terms of GNU GPL v3}}

|<ref name="Marco-SolaSammeth2012">{{cite journal|last1=Marco-Sola|first1=Santiago|last2=Sammeth|first2=Michael|last3=Guigó|first3=Roderic|last4=Ribeca|first4=Paolo|title=The GEM mapper: fast, accurate and versatile alignment by filtration|journal=Nature Methods|volume=9|issue=12|year=2012|pages=1185–1188|issn=1548-7091|doi=10.1038/nmeth.2221|pmid=23103880|s2cid=2004416}}</ref>

|2012

Line 911 ⟶ 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 940 ⟶ 964:

| {{yes}}

| {{yes}}

| {{noyes}}

| {{free}}, [[GNU General Public License|GPL]]

|<ref>{{cite journal|last1=Kielbasa|first1=S.M.|last2=Wan|first2=R.|last3=Sato|first3=K. |last4=Horton|first4=P.|last5=Frith|first5=M.C.|title=Adaptive seeds tame genomic sequence comparison|journal=Genome Research|volume=21|issue=3|year=2011|pages=487–493|pmid=21209072|pmc=3044862|doi=10.1101/gr.113985.110}}</ref>

Line 992 ⟶ 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=mpscanAlgorithms in Bioinformatics |chapter=Mpscan: Fast Localisation of Multiple Reads in Genomes|journal=Algorithms in Bioinformatics|volume=5724|year=2009|pages= 246–260|doi=10.1007/978-3-642-04241-6_21|series=Lecture Notes in Computer Science|bibcode=2009LNCS.5724..246R|isbn=978-3-642-04240-9|citeseerx=10.1.1.156.928|s2cid=17187140 }}</ref>

| 2009

|-

Line 1,152 ⟶ 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 1,181 ⟶ 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 1,195 ⟶ 1,220:

| {{No}}

|

|<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=free}}</ref>

| 2009-2010

|-

Line 1,207 ⟶ 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=free}}</ref>

|

|-

Line 1,221 ⟶ 1,246:

|-

|SparkBWA

| Integrates the [[Burrows-WheelerBurrows–Wheeler Aligner]]—BWA (BWA) on an [[Apache Spark]] framework running atop [[Apache Hadoop|Hadoop]]. Version 0.2 of October 2016, supports the algorithms BWA-MEM, BWA-backtrack, and BWA-ALN. All of them work with single-reads and paired-end reads.

| {{yes}}

| {{partial|Low quality bases trimming}}

Line 1,227 ⟶ 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 1,257 ⟶ 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 1,291 ⟶ 1,316:

|-

| VelociMapper

| FPGA-accelerated reference sequence alignment mapping tool from [[TimeLogic]]. Faster than [[Burrows-WheelerBurrows–Wheeler transform]]-based algorithms like BWA and Bowtie. Supports up to 7 mismatches and/or indels with no performance penalty. Produces sensitive Smith-WatermanSmith–Waterman gapped alignments.

| {{yes}}

| {{yes}}

Line 1,311 ⟶ 1,336:

|-

| ZOOM

| 100% sensitivity for a reads between 15- and 240 bp with practical mismatches. Very fast. Support insertions and deletions. Works with Illumina & SOLiD instruments, not 454.

|

|

Line 1,325 ⟶ 1,350:

==References==

{{Reflist|2}}

[[Category:Database-related lists|Seq]]

{{DEFAULTSORT:List Of Sequence Alignment Software}}

[[Category:BioinformaticsGenetics-related softwarelists|Sequence]]

[[Category:Lists of bioinformatics software|Sequence alignment software]]