In my phytools package
(http://cran.r-project.org/web/packages/phytools/index.html) there is a
function reroot() that is really just a simple wrapper around root()
that allows you to root along internal or terminal edges (rather than
only at nodes).
In your example, assuming that the node 500 is tipward of 174 in the
tree, to re-root the tree halfway along the edge leading to node number
500 (in tree$edge), you would just do:
rooted.tree<-reroot(tree,node.number=500,position=tree$edge.length[tree$edge[,2]==500]/2)
I think.
All the best, Liam
--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://phytools.blogspot.com
On 10/25/2011 10:44 AM, Ondřej Mikula wrote:
Hello,
I have an unrooted tree, but I know that basal dichotomy is between nodes
labeled "174" and "500". I am wandering how to indicate it in the object of
class 'phylo'. I tried 'root' function of 'ape' but with no success.
I will be grateful for any advice. Best wishes
Ondrej Mikula
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