Hi David. Sounds like you want drop.tip from ape to get rid of the outgroup. You need only pass in the tree and the outgroup(s) name(s).
extract.clade will so something similar, but you need to calculate the mrca for each tree first to pass in the node id. HHT. JWB ________________________________________ Joseph W. Brown Post-doctoral Researcher, Smith Laboratory University of Michigan Department of Ecology & Evolutionary Biology Room 2071, Kraus Natural Sciences Building Ann Arbor MI 48109-1079 josep...@umich.edu > On 8 May, 2017, at 07:31, David Buckley <dbuck...@mncn.csic.es> wrote: > > Probably a very easy question, but I could’t find a straightforward answer > for it… > I have a posterior distribution of trees all rooted with a > not-so-closely-related outgroup. I’d like to perform some diversification > analyses (LTT, etc.) just for the ingroup, obviating the outgroup. Is there > an easy way to extract the ingroup (or remove the outgroup) from all the > trees before performing the analyses? I have tried to do it ‘manually’, > deleting the outgroup taxa in Mesquite, but it looks to me that the LTT plots > are still considering some branch lengths from the ingroup to the outgroup > clade (kind of considering a stem-origin, not a crown-origin for the ingroup > clade…). > > Sorry if the question is too naïve… > > best > > david > > > > David Buckley > Dpt. Biodiversity and Evolutionary Biology > Museo Nacional de Ciencias Naturales, MNCN-CSIC > c/José Gutiérrez Abascal 2 > 28006-Madrid > Spain > Phone: +34 91 411 13 28 ext. 1126 > dbuck...@mncn.csic.es > https://www.researchgate.net/profile/David_Buckley4 > <https://www.researchgate.net/profile/David_Buckley4> > http://scholar.google.com/citations?user=qEFTmfkAAAAJ&hl=en > <http://scholar.google.com/citations?user=qEFTmfkAAAAJ&hl=en> > > > > > > > > > > > > > > [[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/ [[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/
