Dear Liam and Klaus,
thanks a lot for your suggestions. "174" and "500" are actually labels of
the nodes, but I used their numbers instead and it works well.
All the best
Ondrej
On 25 October 2011 17:28, Liam J. Revell wrote:
> On seeing this email, I also realized that to have node numbers up
On seeing this email, I also realized that to have node numbers up to
500, that you must have >174 tips (i.e., node number 174 is actually a
tip), meaning the code I gave before should be:
rooted.tree<-reroot(tree,node.number=174,position=tree$edge.length[tree$edge[,2]==174]/2)
I hope this hel
Dear Ondrej,
there is also a function midpoint in phangorn, which roots the trees
in the middle of the longest path. Maybe you are lucky and your edge
(500, 174) is one in the middle.
Regards,
Klaus
On 10/25/11, Liam J. Revell wrote:
> In my phytools package
> (http://cran.r-project.org/web/pac
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
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
--
Institu
