Hi Jesse, there is a function maxCladeCred() to compute maximum-clade-credibility in phangorn, if you prefer doing it in R. In the package are several distances between trees implemented see ?RF.dist (treespace uses them internally). Klaus

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On Wed, Jul 26, 2017 at 11:06 AM, Santiago Sánchez < santiago.snc...@gmail.com> wrote: > Hi Jesse, > > As Eduardo says, if in fact you want to see how different trees are from a > "consensus", something that you could try is find the > maximum-clade-credibility (MCC) tree (you can do this with treeAnnotator > from BEAST). This will be a fully bifurcating tree and is essentially the > tree in the posterior distribution that maximizes the overall clade > posterior probabilities (e.g. sum(posterior)). Once you have the MCC tree, > you can use the Robinson-Foulds distance metric (there is a function in > phytools) to compare all the topologies in your posterior distribution. The > trees with the lowest values will be the most incongruent with respect to > the MCC tree. Just remember to exclude the burnin. > > Cheers, > Santiago > > On Wed, Jul 26, 2017 at 6:01 AM <r-sig-phylo-requ...@r-project.org> wrote: > > > Send R-sig-phylo mailing list submissions to > > r-sig-phylo@r-project.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > or, via email, send a message with subject or body 'help' to > > r-sig-phylo-requ...@r-project.org > > > > You can reach the person managing the list at > > r-sig-phylo-ow...@r-project.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of R-sig-phylo digest..." > > > > > > Today's Topics: > > > > 1. selecting a set of incongruent trees from a posterior > > distribution (Jesse Delia) > > 2. Re: selecting a set of incongruent trees from a posterior > > distribution (Eduardo Ascarrunz) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 25 Jul 2017 16:16:30 -0400 > > From: Jesse Delia <jdeli...@gmail.com> > > To: R-sig-phylo@r-project.org > > Subject: [R-sig-phylo] selecting a set of incongruent trees from a > > posterior distribution > > Message-ID: > > < > > ca+lom6ehmv6c2v_lso8b2sdqqvoqwfcrl56-4jhcmicvjyv...@mail.gmail.com> > > Content-Type: text/plain; charset="UTF-8" > > > > Dear list, > > > > Does anyone know of a function or script that could select a set of the > > most incongruent trees from a list of trees? Maybe I missed a post, but > > haven't found anything. > > > > I running mixed models, which take a lot of computational space on my lap > > top. In effort to account for phylogenetic uncertainty, without having to > > run 100s of chains, I figured maybe i could run models across a (much) > > shorter list that accounts for more diversity in tree shape observed > within > > the posterior distribution. Not sure if this makes sense, and/or is > > extremely complicated? > > > > Thanks for you time! > > > > Jesse > > > > [[alternative HTML version deleted]] > > > > > > > > ------------------------------ > > > > Message: 2 > > Date: Wed, 26 Jul 2017 11:33:12 +0200 > > From: Eduardo Ascarrunz <ear...@gmail.com> > > To: Jesse Delia <jdeli...@gmail.com> > > Cc: R Sig Phylo Listserv <R-sig-phylo@r-project.org> > > Subject: Re: [R-sig-phylo] selecting a set of incongruent trees from a > > posterior distribution > > Message-ID: > > < > > cakxhxpxj_8ucosjt-bzpzvsn+5quet9vxnd4ssd4bqaq-fp...@mail.gmail.com> > > Content-Type: text/plain; charset="UTF-8" > > > > Hi Jesse, > > > > Do you want to select the trees that are most incongruent with some sort > of > > average of the tree distribution? The `treespace`and `phytools` packages > > have functions that compute average trees with different metrics, and > they > > also allow you to measure the distance between each tree and the average > > tree. > > > > Cheers, > > > > Eduardo > > > > 2017-07-25 22:16 GMT+02:00 Jesse Delia <jdeli...@gmail.com>: > > > > > Dear list, > > > > > > Does anyone know of a function or script that could select a set of the > > > most incongruent trees from a list of trees? Maybe I missed a post, but > > > haven't found anything. > > > > > > I running mixed models, which take a lot of computational space on my > lap > > > top. In effort to account for phylogenetic uncertainty, without having > to > > > run 100s of chains, I figured maybe i could run models across a (much) > > > shorter list that accounts for more diversity in tree shape observed > > within > > > the posterior distribution. Not sure if this makes sense, and/or is > > > extremely complicated? > > > > > > Thanks for you time! > > > > > > Jesse > > > > > > [[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-ph...@r-project.org/ > > > > > > > [[alternative HTML version deleted]] > > > > > > > > ------------------------------ > > > > Subject: Digest Footer > > > > _______________________________________________ > > R-sig-phylo mailing list > > R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > > ------------------------------ > > > > End of R-sig-phylo Digest, Vol 114, Issue 10 > > ******************************************** > > > -- > ========================== > Santiago Sanchez-Ramirez, PhD > Postdoctoral Associate > Ecology and Evolutionary Biology > University of Toronto > ========================== > > [[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-ph...@r-project.org/ > -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston http://www.phangorn.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/