Hi Thiago.
You could do something like this using phytools & ape. For genus name
"Genus1" (assuming genus & species names are separated by a "_" character):
x<-grep("Genus1_",tree$tip.label)
... gives you the indices in tree$tip.label for everything in "Genus1".
y<-findMRCA(tree,tree$tip.label[x])
... gives you the node number for the ancestor of "Genus1".
tree<-bind.tip(tree,"Genus1_newsp",where=y)
... attaches the new tip to the root of "Genus1".
Note that this will only work if you have multiple species in each genus
that you want to add to. If not, then the MRCA of the genus will not be
defined. In that case, you could, for instance, add the new tip 1/2 way
along the terminal edge leading to the one species in "Genus1". E.g.:
if(length(x)==1){
tree<-bind.tip(tree,"Genus1_newsp",where=x,
position=0.5*tree$edge.length[which(tree$edge[,2]==x)])
}
It would be straightforward to automate this if you have to iterate
across many samples. Let me know if you need help with that.
All the best, Liam
Liam J. Revell, Assistant 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 10/31/2013 1:41 PM, Thiago A. Pires wrote:
Dear list members,
I need to add a list of 230 species in a
phylogenetic tree. Is there a logical way to add the species to the root of
the
genre to which it belongs, in a systematic way, that is, to make
a
function recognizes the name of the
genre to which the species belongs, and so it adds the species to that
root? I can name the roots of the
genre of the tree, if necessary.
Thanks in advance
T.
_____________________________________________________________
Thiago Augusto Pires
Mestrando - PPG Ecologia - Instituto de Biologia - UNICAMP
Master Student - Ecology Program - Biology Institute - UNICAMP
Collaborator Researcher - Laboratory of Ecology and Systematics - UNIFESP
Email: pires.thiagoaugu...@gmail.com
Home Page:
http://thiagoaugustopires.wix.com/naturevisions
CV Lattes:
http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4298681Z0
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