Hello, you may have a look at find.clusters (K-means based clustering) and gengraph (transitive graph clusters) in adegenet too.
Cheers Thibaut ________________________________________ From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Sam Brown [s_d_j_br...@hotmail.com] Sent: 14 March 2013 21:18 To: r-sig-phylo@r-project.org; gian.benu...@gmail.com Subject: Re: [R-sig-phylo] How to cluster sequences in different OTUs > Date: Thu, 14 Mar 2013 10:21:39 +0100 > From: Gian Maria Niccol? Benucci <gian.benu...@gmail.com> > To: r-sig-phylo@r-project.org > Subject: [R-sig-phylo] How to cluster sequences in different OTUs > > Hi everyone, > > I was wondering is exist a function that is able to generate OTUs from a > sequences database. > Thank you very much in advance, > > -- > Gian Hi Gian The function tclust() in the spider package (on CRAN) groups sequences based on their genetic distance below a given threshold. If you want a something with likelihoods measured for it, check out the gmyc() function in the splits package (hosted on R Forge: https://r-forge.r-project.org/projects/splits/). This requires an ultrametric tree to create the the OTUs. There may be others, but these two come immediately to mind. All the best. Sam Samuel Brown Postgraduate Student Bio-Protection Research Centre PO Box 84 Lincoln University Lincoln 7647 Canterbury New Zealand sam.br...@lincoln.ac.nz http://www.the-praise-of-insects.blogspot.com [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
