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| [[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
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| [[PatternHunter]]
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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
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| {{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
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| {{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
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| <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
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| {{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
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<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
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