Re: [R] Clustering and bootstrap

From: Huntsinger, Reid <reid_huntsinger_at_merck.com>
Date: Thu 22 Sep 2005 - 04:46:50 EST


I suppose you could average the distance matrices, getting a distance matrix, and then apply hierarchical clustering... or threshold the average distance matrix at a sequence of values and compute connected components for each... that sounds like it's in the spirit of a "majority-rule consensus tree" though I don't know what that is.

Reid Huntsinger

-----Original Message-----
From: r-help-bounces@stat.math.ethz.ch
[mailto:r-help-bounces@stat.math.ethz.ch] On Behalf Of Eric Pante Sent: Wednesday, September 21, 2005 12:50 PM To: r-help@stat.math.ethz.ch
Subject: [R] Clustering and bootstrap

Dear Listers,

I emailed the list a few days ago about how to bootstrap a community matrix (species by sites) and get a consensus tree with node support. A friend pointed out that a similar question remained unanswered in 2004. I wish to re-word my question: is anyone aware of a package / method to obtain a majority-rule consensus tree from x distance matrices ? Is anyone using R to generate phylogenetic trees with node support ?

thanks for your time and consideration,
Eric P.

Eric Pante



Graduate Student in Marine Biology
Grice Marine Laboratory
205 Fort Johnson Road, Charleston SC 29412
	"On ne force pas la curiosite, on l'eveille ..."
	Daniel Pennac


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R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Thu Sep 22 04:51:44 2005

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