Miguel Verdu --
> I want to perform a mothur-like OTU-based approach, but based on phylogenetic
> instead of DNA sequence distances. Is there any way to cluster tips of a tree
> into OTUs determined by a threshold of phylogenetic distances?. In other
> words, I want to collapse all the tips connected with distances less than X
> into the same OTUs.
I don't know which R program will do this (probably just a one-line "if"
command) but the obvious method would be to take the distance matrix and reduce
all the elements of it that are less than X to 0.000. Then run any distance
method.
J.F.
----
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
(from 1 October 2012 to 10 December 2012 on sabbatical leave at)
Department of Statistics, University of California, Berkeley, 367 Evans Hall,
Berkeley, CA 94710
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