[R-sig-phylo] extracting information about n-order nodes

François Michonneau francois.michonneau at gmail.com
Thu May 13 17:47:28 CEST 2010


Hi Eric,

  The package phylobase [1] provides the function descendants and
ancestors which for a given node returns the nodes for all the
descendants or ancestors. So it will allow you to determine the order of
your nodes based on the number of descendants or ancestors which are
associated with them.

  Furthermore, if you import your tree as a NEXUS file, phylobase can
store bootstrap value supports as data with their associated node number
as row names. You'll need to use:

tr <- readNexus(yourFile, check.node.labels="asdata")

and use the function tdata to retrieve your support values:

tdata(tr, "internal")

  Let me know if you have any questions.

  Cheers,
  -- François 

[1] install.packages("phylobase", repos="http://r-forge.r-project.org")

On Thu, 2010-05-13 at 09:25 -0500, Eric Pante wrote:
> Dear listers,
> 
> I would like to extract bootstrap support values for all nodes of a  
> specific order. I other terms, I want to get a vector of bootstrap  
> support values for 1st order nodes, then 2nd order nodes, etc... I  
> would like to assess the effect of adding genes to resolving deep  
> phylogenetic relationships. Any hint would be very appreciated!
> 
> Best regards, eric
> 
> Eric Pante
> ----------------------------------------------------------------
> Department of Biology
> University of Louisiana at Lafayette
> P.O. Box 42451, Lafayette, LA 70504
> Lab: (337) 482-6494
> Web: www.ull.edu/~egp0628
> ----------------------------------------------------------------
> 
> "On ne force pas la curiosite, on l'eveille ..."
> Daniel Pennac
> 
> 
> 
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