Dear Laura.

`I also just posted a possible solution to my blog here:`

`http://blog.phytools.org/2017/06/generating-set-of-random-resolutions-of.html.`

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All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 6/21/2017 11:02 AM, Liam J. Revell wrote:

[This sender failed our fraud detection checks and may not be who they appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing] Hi Laura. The phytools functions resolveNode and resolveAllNodes could be used. They resolve either a single node in all possible ways; or all nodes in all possible ways, returning a "multiPhylo" object. Note that in the latter case the number of trees can be quite large. From the phytools doc: "For resolveNode applied to a multifurcation with n descendants, the number of resolved trees will be equal to the number of possible rooted trees of n taxa. (For instance, three for a trifurcation, 15 for a quadrifurcation, and so on.) For resolveAllNodes the number of fully resolved trees will be equal to the product of numbers for resolveNode applied to each multifurcation separately. (For instance, 45 for a tree containing one trifurcation and one quadrifurcation.)" To get a random set of resolved trees, rather than all possible trees (because this number can be high), you could start with one multifurcating node in the tree, resolve it in all ways using resolveNode, pick one of those resolutions, then move to the next node & so on. I will try to post a formal solution & then share it to the list. All the best, Liam Liam J. Revell, Associate Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 6/21/2017 10:38 AM, Laura Jackson wrote:Hi all, I am using the ape package to randomly resolve polytomies using 'multi2di' and wondering if there is a way to use this function to get a single output tree file that contains multiple different randomly resolved trees using some number of resamplings? Thanks, -Laura_______________________________________________ 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/

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