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?


> On Dec 14, 2016, at 12:41 PM, Keith Barker <> 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
>>      [[alternative HTML version deleted]]
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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
> University of Minnesota
> 140 Gortner Laboratory
> 1479 Gortner Ave
> Saint Paul, MN 55108
> 612.624.2737 (phone)
> 612.624.6777 (fax)
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