Hi everyone,
I am simulating characters evolving in a phylogetic tree under a number of
models and using those characters to build another tree using parsimony.
I would like, then, to measure how similar are the recovered trees when
compared to the original ones, taking only topology into
Hi Bruno.
RF.dist in the phangorn package computes Robinson-Foulds distance
(http://en.wikipedia.org/wiki/Robinson-Foulds_metric). This is not
obvious, but (unless you want the position of the root to affect the
score) you should probably unroot your trees before using RF.dist, e.g.:
Hi Liam,
Many thanks.
Just an additional question related to Robinson-Foulds distance. It seems
RF.dist() requires the compared trees to be binary. Is there any standard
procedure for dealing with multifurcating trees?
Best,
Bruno
--
Bruno A. S. de Medeiros
PhD Student - Farrell Lab
Harvard
