List of sequence alignment software: Difference between revisions

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Latest revision as of 17:48, 23 June 2025

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! Year

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| [[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

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| [[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

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| 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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| 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

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| 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

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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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| [[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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| 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]] || 1993-20162023 ||

|-

| 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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| {{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]]

|

|

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| {{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

Line 1,344 ⟶ 1,352:

{{Reflist}}

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

[[Category:Genetics-related lists|Sequence]]

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