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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
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| USEARCH
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| 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
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| DNADot
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| [[MUSCLE (alignment software)|MUSCLE]]
| Progressive-iterative alignment (v3), Probabilistic/consistency (v5) || Both || Local or global || R. Edgar || 2004 || Public ___domain
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| Opal
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