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> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ > > -- > 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) > barke...@umn.edu > http://www.tc.umn.edu/~barke042 > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
