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"
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
Dear list members,
I was wondering if somebody already tried (or knows somebody who did)
using R to access CIPRES using the RESTful API? I think it's a great
solution for people with limited resources.
https://www.phylo.org/restusers/docs/guide.html#SampleCode
Best wishes,
Andreas
