Dear Roger, ggtree can parse BEAST output and visualize BEAST statistics, see the document: http://www.bioconductor.org/packages/3.2/bioc/vignettes/ggtree/inst/doc/ggtree.html#annotating-tree-with-beast-output
Bests, Guangchuang On Thu, Dec 10, 2015 at 7:00 PM, <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. Re: Plotting sampled-ancestor trees in R (Roger Close) > 2. Implementation of Mir et al.'s (2013) tree balance index? > (Gabriel Yedid) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 9 Dec 2015 15:50:11 +0000 > From: Roger Close <roger.cl...@gmail.com> > To: David Bapst <dwba...@gmail.com> > Cc: R Sig Phylo Listserv <r-sig-phylo@r-project.org> > Subject: Re: [R-sig-phylo] Plotting sampled-ancestor trees in R > Message-ID: > <CAFauv= > ubz3yncju8j+jgpxpfop0na4yy_3o7bayd7csxbvf...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Dave, Emmanuel and Joseph, > > Thanks very much for your suggestions. The output of BEAST, at least, is an > ordinary Newick/NEXUS file with ancestors represented as tips on the ends > of zero-length branches (see attached). > > One way to proceed would be to drop the tips that correspond to ancestors > and then add them back on using edge labels. However, I see that paleotree > designates ancestors using $anag.tips; is there a tool for plotting this > type of tree? > > Cheers, > Roger > > > > --- > Roger Close, Postdoctoral Research Associate > Department of Earth Sciences, Oxford University > South Parks Road > Oxford OX1 3AN > United Kingdom > > On 8 December 2015 at 18:56, David Bapst <dwba...@gmail.com> wrote: > > > Hi Roger, > > > > I'm not aware of any existing solution. Could you send around a small > > example of the data format of an output sampled ancestor tree from > > BEAST or MrBayes? Are they just typical Newick/NEXUS format with > > ancestors indicated tipis with zero-length branches or something more > > complicated? > > > > Remarkably I've not looked at the formatting of one, but obviously > > plotting SA trees is something the community will need in the near > > future. > > > > Cheers, > > -Dave > > > > On Tue, Dec 8, 2015 at 5:46 AM, Roger Close <roger.cl...@gmail.com> > wrote: > > > Hi all, > > > > > > Does anyone know of a way to plot sampled-ancestor trees in R such that > > > ancestors lie on branches, rather than being zero-length terminals that > > > follow a bifurcation? > > > > > > Many thanks, > > > Roger > > > > > > --- > > > Roger Close, Postdoctoral Research Associate > > > Department of Earth Sciences, Oxford University > > > South Parks Road > > > Oxford OX1 3AN > > > United Kingdom > > > > > > [[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/ > > > > > > > > -- > > David W. Bapst, PhD > > Adjunct Asst. Professor, Geology and Geol. Eng. > > South Dakota School of Mines and Technology > > 501 E. St. Joseph > > Rapid City, SD 57701 > > > > http://webpages.sdsmt.edu/~dbapst/ > > http://cran.r-project.org/web/packages/paleotree/index.html > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > https://stat.ethz.ch/pipermail/r-sig-phylo/attachments/20151209/47c627ad/attachment-0001.html > > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: sa.tree.tre > Type: application/octet-stream > Size: 1919 bytes > Desc: not available > URL: < > https://stat.ethz.ch/pipermail/r-sig-phylo/attachments/20151209/47c627ad/attachment-0001.obj > > > > ------------------------------ > > Message: 2 > Date: Thu, 10 Dec 2015 15:50:52 +0800 > From: Gabriel Yedid <gyedi...@gmail.com> > To: r-sig-phylo <r-sig-phylo@r-project.org> > Subject: [R-sig-phylo] Implementation of Mir et al.'s (2013) tree > balance index? > Message-ID: > <CAD= > v+xfxrpyofojk6q_77v22dg1lwc-s248xoj-xzw0sgur...@mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hello all, > > Is there any R implementation yet of the tree balance metric described in: > > > Mir, Arnau, Francesc Rossell?, and Lidia Rotger. "A new balance index > for phylogenetic trees." Mathematical biosciences 241.1 (2013): > 125-136. > > > cheers, > > Gabe > > > > ------------------------------ > > 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 95, Issue 6 > ****************************************** > -- --~--~---------~--~----~------------~-------~--~----~ Guangchuang Yu, PhD Candidate State Key Laboratory of Emerging Infectious Diseases School of Public Health The University of Hong Kong Hong Kong SAR, China www: http://guangchuangyu.github.io -~----------~----~----~----~------~----~------~--~--- [[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/
