Frank:

You can import all of the trees into one or more multiPhylo objects, then use the ape functions prop.part or prop.clades (depending on what you want to do) to summarize different subsets (e.g., from different analyses). Here is an example with simulated trees:


x<-rmtree(50,100)
plot(x[[1]])
nodelabels(prop.clades(x[[1]],x))
y<-rep(x[1],50)
plot(x[[1]])
nodelabels(prop.clades(x[[1]],c(x,y)))

The first part just creates a bunch of random trees, so most nodes will only be supported by around 1-4 or so trees. The second part just repeats tree one 50 times, and when you label the nodes with trees x+ tres yy, you get 50 plus the number of trees from part 1. That should give you the idea.

You can find the shared clades from the "best" trees (if you are doing ML) by first calculating the strict consensus using the consensus function in ape.

Hope that helps,
Keith

On 12/14/16 10:19 AM, Frank T Burbrink wrote:
Hello,

I have one question

Is there a method to compare the support values (either bootstraps or Pp) 
across all shared clades between two or more different trees having identical 
taxa? I believe this method would have to first identify the shared clades and 
then determine the measure of support at each shared node.

Thank you,

Frank

Frank T. Burbrink, Ph.D.
Associate Curator
Department of Herpetology
American Museum of Natural History
Central Park West at 79th Street
New York, NY 10024-5192

fburbr...@amnh.org<mailto:fburbr...@amnh.org>

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F. Keith Barker, Ph.D.
Associate Professor, Department of Ecology, Evolution and Behavior
Curator of Genetic Resources, and
Interim Curator of Birds, Bell Museum of Natural History
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