List of sequence alignment software: Difference between revisions

Revision as of 03:16, 6 August 2024

Latest revision as of 17:48, 23 June 2025

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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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|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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| 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<ref>{{Cite journal |last=Powell |first=David R. |last2=Allison |first2=Lloyd |last3=Dix |first3=Trevor I. |date=2005 |editor-last=Webb |editor-first=Geoffrey I. |editor2-last=Yu |editor2-first=Xinghuo |title=Modelling-Alignment for Non-random Sequences |url=https://link.springer.com/chapter/10.1007/978-3-540-30549-1_19 |journal=AI 2004: Advances in Artificial Intelligence |language=en |___location=Berlin, Heidelberg |publisher=Springer |pages=203–214 |doi=10.1007/978-3-540-30549-1_19 |isbn=978-3-540-30549-1}}</ref>|| 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<ref>{{Cite journal |last=Powell |first=DAVID R. |last2=Allison |first2=LLOYD |last3=Dix |first3=TREVOR I. |date=2000-12-07 |title=Fast, Optimal Alignment of Three Sequences Using Linear Gap Costs |url=https://www.sciencedirect.com/science/article/pii/S0022519300921775 |journal=Journal of Theoretical Biology |volume=207 |issue=3 |pages=325–336 |doi=10.1006/jtbi.2000.2177 |issn=0022-5193}}</ref>|| 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]]

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| [[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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| [[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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{{Reflist}}

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

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

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