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 >
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