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

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/