HI Max, Not entirely sure if this is what you want but i did come across a script to extract direct sister pairs (tips) in a tree
>From the dryad supplement of Grossenbacher D, Briscoe Runquist R, Goldberg >EE, Brandvain Y (2015) Geographic range size is predicted by plant mating >system. Ecology Letters 18(7): 706-713. https://doi.org/10.5061/dryad.hv117/6 <https://doi.org/10.5061/dryad.hv117/6> The script grabs sister pairs across a sample of tree and gives their distance - i.e. pairs of tips that are monophyletic here is the code I have from that script (might be worth getting it from the source script again) ##### # Get all sisters GetSisters = function(TREE){ tips = TREE$edge[TREE$edge[,2]<=length(TREE$tip.label),] sis.nodes = tips[duplicated(tips[,1]),1] tmp=data.frame(cbind(sis.nodes,do.call(rbind,lapply(sis.nodes,function(NODE){ this = TREE$edge[,1]==NODE c(TREE$edge[this,2][1:2],sum(TREE$edge.length[this][1:2])) })))) colnames(tmp) = c("internal","A","B","dist") tmp$a = TREE$tip.label[tmp$A]; tmp$b = TREE$tip.label[tmp$B] tmp } ##### Hope it helps Cheers Pete ======================================= Peter F Cowman, Ph.D. Senior Research Fellow in Ecosystem Dynamics ARC Discovery Fellow (DECRA) ARC Centre of Excellence for Coral Reef Studies <https://www.coralcoe.org.au/> James Cook University, Townsville, QLD, 4811, Australia Office: +61 7 4781 3194 | Rm 128 Bld DB019 Email: peter.cow...@jcu.edu.au <mailto:peter.cow...@jcu.edu.au> Twitter: @pete_cowman ORCID ID: orcid.org/0000-0001-5977-5327 <http://orcid.org/0000-0001-5977-5327> > On 10 Jan 2020, at 07:36, Max Shpak <shpak....@gmail.com> wrote: > > If I have an object of class "phylo" in the ape, with attributes edge, > Nnode, node.label, and tip.label, is there some straightforward way for me > to extract a list of sister taxon pairs (whether the sister taxa are two > edges or an edge and a node)? > > I wrote to E. Paradis (the author of ape), and he said that he didn't know > of a direct way to do this, but it may be possible through some > manipulation of the mrca functions. > > Does anybody on this board have any suggestions for how to go about this? > > Thank you, Max Shpak > > -- > ======================= > Max Shpak, Ph.D. > Center for Systems and Synthetic Biology > University of Texas at Austin > Austin, TX 78712 > > [[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/ [[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/
