Hi Liam, I was trying to get this to work on my tree, but it seems that it doesn't work for larger phylogenies (~1000 tips)? I get the following error message,..."Error in allTrees(n, TRUE, dd) : That would generate 7905853580625 trees, and take up more than 7905853581 MB of memory! "
I have attached my phylogeny here. I am trying to get even 10 different randomly resolved trees. Is this possible with my phylogeny? Thanks. -Laura On Wed, Jun 21, 2017 at 11:08 AM, Laura Jackson <jacksonlaura...@gmail.com> wrote: > Liam, > > Thanks so much for your reply and for the blog post, I was able to get it > working. > > -Laura > > On Wed, Jun 21, 2017 at 10:35 AM, Liam J. Revell <liam.rev...@umb.edu> > wrote: > >> Dear Laura. >> >> I also just posted a possible solution to my blog here: >> http://blog.phytools.org/2017/06/generating-set-of-random-re >> solutions-of.html. >> >> 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/ >>> >> > > > -- > *Laura M. Jackson* > PhD Candidate > Department of Biology > 185 Churchill Haines > University of South Dakota > 414 E. Clark St. > Vermillion SD 57069-1746 > Email: laura.jack...@usd.edu > -- *Laura M. Jackson* PhD Candidate Department of Biology 185 Churchill Haines University of South Dakota 414 E. Clark St. Vermillion SD 57069-1746 Email: laura.jack...@usd.edu
Eel_phylogeny.phy
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