Sequence clustering: Difference between revisions

Revision as of 07:05, 24 September 2015

Revision as of 14:23, 2 June 2016

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== Sequence clustering algorithms and packages ==

* Starcode<ref>{{cite web|url=http://www.github.com/gui11aume/starcode|title=Starcode repository}}</ref>: a fast sequence clustering algorithm based on exact all-pairs search.<ref>{{cite journal

|title=Starcode: sequence clustering based on all-pairs search

|author=Zorita E, Cuscó P, Filion GJ.

|journal=Bioinformatics.

|date=Jun 2015 |volume=31

|issue=12 |pages=1913-1919

|doi=10.1093/bioinformatics/btv053

|pmid=25638815}}</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>{{cite journal

|title=OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy.