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
Hi Eric, I work about bootstrap and clustering and I also write R-code about that, which is not documented up to now though. You may have a look at http://www.homepages.ucl.ac.uk/~ucakche/papers/classbrd.ps I also worked about species by site data and there is a parametric bootstrap test implemented as function prabtest in package prabclus. You may have a look at that, too. However, all of this does not really fit to your new question and I am not sure whether I have anything of interest to you. Feel free to contact me if you can somehow relate your problem to my work mentioned above. Best, Christian On Wed, 21 Sep 2005, Eric Pante wrote:> 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 > > ______________________________________________ > R-help at 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 >*** --- *** Christian Hennig University College London, Department of Statistical Science Gower St., London WC1E 6BT, phone +44 207 679 1698 chrish at stats.ucl.ac.uk, www.homepages.ucl.ac.uk/~ucakche
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 at stat.math.ethz.ch [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Eric Pante Sent: Wednesday, September 21, 2005 12:50 PM To: r-help at 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 ______________________________________________ R-help at 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
> From: Eric Pante <ericpante at hotmail.com> > > 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 ? >This is not (currently ;)) an R solution nor bootstrapping, instead using a pretty general reversible-jump type Gibbs sampler (see P 11 onward and refs) http://eprint.uq.edu.au/archive/00001138/