Hi Jake,

What you describe looks very musch like the Lento method implemented in the function lento() in phangorn. consensusNet(), also in phangorn, implements something similar: the consensus network.


prop.part(), in ape, is the function behind the two previous ones. bitsplits() is more efficient with a different output format. There are functions as.prop.part() and as.bitsplits() to convert among these classes.

Best,

Emmanuel

Le 14/12/2016 à 19:01, Jacob Berv a écrit :
To clarify - the idea here is that you are asking which clades appear in 
’subordinate’ trees relative to clades that exist in a consensus tree, and then 
interrogating the support values of the shared clades which exist in the 
’subordinate’ trees? So for example, clade A appears in consensus tree X, and 
also appears in gene trees 1-5 - so this will give me the summary of the 
support values for clade A in gene trees 1-5?

Seems like this would be a useful function to interrogate support values among 
clades recapitulated in gene trees relative to a species tree. Would there be 
an analogue for clades that exist in your consensus that don’t exist in 
’subordinate’ trees?

Jake


On Dec 14, 2016, at 12:41 PM, Keith Barker <barke...@umn.edu> wrote:

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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