Sequence clustering: Difference between revisions

Revision as of 23:34, 16 April 2020

Revision as of 04:06, 16 September 2020

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* Starcode:<ref>{{cite web|url=https://github.com/gui11aume/starcode|title=Starcode repository|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 (Oxford, England) | 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 | issue = | pages = 157 | date = August 2015 | pmid = 26243257 | pmc = 4531804 | doi = 10.1186/s13059-015-0721-2 }}</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 }}</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 }}</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 |accessdate=2004-02-19 |url-status=dead |archiveurl=https://web.archive.org/web/20031206172749/http://bio.informatics.indiana.edu/sunkim/BAG/ |archivedate=2003-12-06 }}</ref>

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* 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/ | titlearchive-date=Index of /pub/nrdb2008-01-01}}</ref> a program for merging trivially redundant (identical) sequences

* CluSTr:<ref>{{cite web |url=http://www.ebi.ac.uk/clustr/ |title=Archived copy |accessdate=2006-11-23 |url-status=dead |archiveurl=https://web.archive.org/web/20060924012903/http://www.ebi.ac.uk/clustr/ |archivedate=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