Editing Sequence clustering (section)

== Sequence clustering algorithms and packages ==
{{directory|date=September 2018}}
* CD-HIT<ref name=cdhit/>
* [[UCLUST]] in USEARCH<ref name=usearch/>
* Starcode:<ref>{{cite web|url=https://github.com/gui11aume/starcode|title=Starcode repository|website=[[GitHub]]|date=2018-10-11}}</ref> a fast sequence clustering algorithm based on exact all-pairs search.<ref name="pmid25638815">{{cite journal | vauthors = Zorita E, Cuscó P, Filion GJ | title = Starcode: sequence clustering based on all-pairs search | journal = Bioinformatics | volume = 31 | issue = 12 | pages = 1913–9 | date = June 2015 | pmid = 25638815 | pmc = 4765884 | doi = 10.1093/bioinformatics/btv053 }}</ref>
* OrthoFinder:<ref>{{cite web|url=http://www.stevekellylab.com/software/orthofinder|title=OrthoFinder|work=Steve Kelly Lab}}</ref> a fast, scalable and accurate method for clustering proteins into gene families (orthogroups)<ref name="pmid26243257">{{cite journal | vauthors = Emms DM, Kelly S | title = OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy | journal = Genome Biology | volume = 16 | pages = 157 | date = August 2015 | issue = 1 | pmid = 26243257 | pmc = 4531804 | doi = 10.1186/s13059-015-0721-2 | doi-access = free }}</ref><ref name="pmid31727128">{{cite journal | vauthors = Emms DM, Kelly S | title = OrthoFinder: phylogenetic orthology inference for comparative genomics | journal = Genome Biology | volume = 20 | issue = 1 | pages = 238 | date = November 2019 | pmid = 31727128 | pmc = 6857279 | doi = 10.1186/s13059-019-1832-y | doi-access = free }}</ref>
* Linclust:<ref name="pmid29959318">{{cite journal | vauthors = Steinegger M, Söding J | title = Clustering huge protein sequence sets in linear time | journal = Nature Communications | volume = 9 | issue = 1 | pages = 2542 | date = June 2018 | pmid = 29959318 | pmc = 6026198 | doi = 10.1038/s41467-018-04964-5 | bibcode = 2018NatCo...9.2542S }}</ref> first algorithm whose runtime scales linearly with input set size, very fast, part of [http://mmseqs.org/ MMseqs2]<ref name="pmid29035372">{{cite journal | vauthors = Steinegger M, Söding J | title = MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets | journal = Nature Biotechnology | volume = 35 | issue = 11 | pages = 1026–1028 | date = November 2017 | pmid = 29035372 | doi = 10.1038/nbt.3988 | hdl = 11858/00-001M-0000-002E-1967-3 | s2cid = 402352 | hdl-access = free }}</ref> software suite for fast, sensitive sequence searching and clustering of large sequence sets
* TribeMCL: a method for clustering proteins into related groups<ref name="pmid11917018">{{cite journal | vauthors = Enright AJ, Van Dongen S, Ouzounis CA | title = An efficient algorithm for large-scale detection of protein families | journal = Nucleic Acids Research | volume = 30 | issue = 7 | pages = 1575–84 | date = April 2002 | pmid = 11917018 | pmc = 101833 | doi = 10.1093/nar/30.7.1575 }}</ref>
* BAG: a graph theoretic sequence clustering algorithm<ref>{{cite web |url=http://bio.informatics.indiana.edu/sunkim/BAG/ |title=Archived copy |access-date=2004-02-19 |url-status=dead |archive-url=https://web.archive.org/web/20031206172749/http://bio.informatics.indiana.edu/sunkim/BAG/ |archive-date=2003-12-06 }}</ref>
* JESAM:<ref>{{cite web|url=http://www.littlest.co.uk/software/bioinf/old_packages/jesam/jesam_paper.html|title=Bioinformatics Paper: JESAM: CORBA software components for EST alignments and clusters|work=littlest.co.uk}}</ref> Open source parallel scalable DNA alignment engine with optional clustering software component
* UICluster:<ref>{{cite web |url=http://ratest.eng.uiowa.edu/pubsoft/clustering/ |title=pedretti@eyeball -- Clustering Page |website=ratest.eng.uiowa.edu |url-status=dead |archive-url=https://web.archive.org/web/20050409134817/http://ratest.eng.uiowa.edu/pubsoft/clustering/ |archive-date=2005-04-09}} </ref> Parallel Clustering of EST (Gene) Sequences
* BLASTClust single-linkage clustering with BLAST<ref>{{cite web|url=https://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html|title=NCBI News: Spring 2004-BLASTLab|work=nih.gov}}</ref>
* Clusterer:<ref>{{cite web|url=http://bugaco.com/bioinf/clusterer/|title=Clusterer: extendable java application for sequence grouping and cluster analyses|work=bugaco.com}}</ref> extendable java application for sequence grouping and cluster analyses
* PATDB: a program for rapidly identifying perfect substrings
* nrdb:<ref>{{Cite web | url=http://blast.wustl.edu/pub/nrdb/ | title=Index of /pub/nrdb| archive-url=https://web.archive.org/web/20080101032917/http://blast.wustl.edu/pub/nrdb/| archive-date=2008-01-01}}</ref> a program for merging trivially redundant (identical) sequences
* CluSTr:<ref>{{cite web |url=http://www.ebi.ac.uk/clustr/ |title=CluSTr |access-date=2006-11-23 |url-status=dead |archive-url=https://web.archive.org/web/20060924012903/http://www.ebi.ac.uk/clustr/ |archive-date=2006-09-24 }}</ref>  A single-linkage protein sequence clustering database from Smith-Waterman sequence similarities; covers over 7 mln sequences including UniProt and IPI
* ICAtools<ref>{{cite web|url=http://www.littlest.co.uk/software/bioinf/old_packages/icatools/|title=Introduction to the ICAtools|work=littlest.co.uk}}</ref> - original (ancient) DNA clustering package with many algorithms useful for artifact discovery or EST clustering
* Skipredudant EMBOSS tool<ref>{{cite web|url=http://bioweb2.pasteur.fr/docs/EMBOSS/skipredundant.html|title=EMBOSS: skipredundant|work=pasteur.fr}}</ref> to remove redundant sequences from a set
* CLUSS Algorithm<ref name="pmid17683581">{{cite journal | vauthors = Kelil A, Wang S, Brzezinski R, Fleury A | title = CLUSS: clustering of protein sequences based on a new similarity measure | journal = BMC Bioinformatics | volume = 8 | pages = 286 | date = August 2007 | pmid = 17683581 | pmc = 1976428 | doi = 10.1186/1471-2105-8-286 | doi-access = free }}</ref> to identify groups of structurally, functionally, or evolutionarily related hard-to-align protein sequences. CLUSS webserver <ref name="prospectus.usherbrooke.ca">{{Cite web | url=http://prospectus.usherbrooke.ca/CLUSS/ | title=CLUSS Home Page}}</ref>
* CLUSS2 Algorithm<ref name="pmid20058485">{{cite journal | vauthors = Kelil A, Wang S, Brzezinski R | title = CLUSS2: an alignment-independent algorithm for clustering protein families with multiple biological functions | journal = International Journal of Computational Biology and Drug Design | volume = 1 | issue = 2 | pages = 122–40 | date = 2008 | pmid = 20058485 | doi = 10.1504/ijcbdd.2008.020190 }}</ref> for clustering families of hard-to-align protein sequences with multiple biological functions. CLUSS2 webserver <ref name="prospectus.usherbrooke.ca"/>
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