Just to add to Joseph's totally correct comment, if your object is of
class "multiPhylo" (that is, a list of trees) you can run:
outgroup<-c("outgroup_A","outgroup_B") ## change to your outgroup(s)
ingroup<-lapply(trees,drop.tip,tip=outgroup)
class(ingroup)<-"multiPhylo"
For some "multiPhylo" objects, for instance those read from a NEXUS
file, you may also want to first run:
trees<-.uncompressTipLabel(trees)
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 5/8/2017 7:01 AM, Joseph W. Brown wrote:
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>
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