Hi all, I just uploaded a new version of phangorn (1.99-7), which does not depend on the rgl package. This should allow phangorn to work on all platforms again. It seems midpoint (phangorn) and midpoint.root (phytools) give the same result, which is reassuring. midpoint seems to be faster for larger trees, let say more than 1000 tips. I also started a small side project ( http://klash.shinyapps.io/shinyTreeViewer/) which is an interactive web-based tree viewer using mainly the ape, phangorn & shiny package. There is a web-server version from http://klash.shinyapps.io/shinyTreeViewer/hosted kindly by RStudio. The github version is more up to date. The tree viewer generates also some R-code to either use it as starting point to generate more complex graphics and/or for reproducible trees. Feedback is welcome. Regards, Klaus
On Fri, Jan 31, 2014 at 1:11 AM, Todd Oakley <todd.oak...@lifesci.ucsb.edu>wrote: > All, > As an update: the script that Liam wrote for midpoint rooting seems to > have worked well for us. I did not numerically test the rooting results, > but they pass the "eye test" (ie they look right to me). I serially rooted > about 100 trees with 50-250 OTU's each, and it was fast, so it was > efficient in our hands. > > Liam has described his process and function on his blog, here: > > http://blog.phytools.org/2014/01/function-for-midpoint- > rooting.html?spref=fb > > > > My application for this is a tool called tab2trees, implemented in Osiris > for Galaxy. It takes a list of newick tree descriptions and visualizes all > the trees in a "pdf book", with one tree per page. Since I often use gene > trees, midpoint rooting is a sensible way to present the trees. Here is a > description of tab2trees (pre-midpoint rooting): > > http://osiris-phylogenetics.blogspot.com/2012/09/tab2trees.html > > > Best wishes, > Todd Oakley, UCSB > > > > > > > On 1/30/2014 3:57 PM, Joe Felsenstein wrote: > >> Liam said: >> >> Joe's correct that this is not yet in our project to create an R >>> interface >>> for PHYLIP (Rphylip, https://github.com/liamrevell/Rphylip). As soon as >>> I >>> get a chance to work on this project today, I will add it. >>> >> That may be hard to do, as Retree is interactive and >> has two levels of menus. >> >> Joe >> ---- >> Joe Felsenstein j...@gs.washington.edu >> Department of Genome Sciences and Department of Biology, >> University of Washington, Box 355065, Seattle, WA 98195-5065 USA >> > > _______________________________________________ > 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 Phylogenomics Lab at the University of Vigo, Spain http://darwin.uvigo.es/kschliep/ [[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/
