Hi Damien & Scott,
I don't know the formula of Icong or MAST, but I'd like to remind you
the function prop.part() that finds all the clades in a set of trees
and returns the compositions and frequencies, eg:
a <- rtree(4)
b <- rtree(4)
prop.part(c(a, b))
1: t2
2: t1
3: t3
4: t4
==> 2 time(s):[1] 1 2 3 4
==> 1 time(s):[1] 2 3 4
==> 2 time(s):[1] 2 3
==> 1 time(s):[1] 1 2 3
This requires the trees to have the same tip labels. It is used in ape
by boot.phylo(), and calls a C code. It doesn't seem to be used by
other developers though it is certainly efficient and may help in many
applications.
Emmanuel
On Tue, 18 Jan 2011 19:46:30 +0100 "Damien de Vienne"
<damien.de-vie...@u-psud.fr> wrote:
Dear Scott,
Having Icong in R would be nice but it is not the case
yet. Sorry...
However if someone has a code (in C for
example) to compute the maximum agreement subtree (MAST) between
two
trees, I would be happy to do the rest in order to have the Icong
index
within R (within the ape package maybe ? And having the simple MAST
calculation there would be also very useful I believe).
Anyway, if you want to automate the calculation of the Icong index
you
can still use PAUP* that calculates the MAST and apply afterwards
the
functions that are in the paper.
If you need help, tell me.
Damien
Le Mar 18 janvier 2011 19:42, Scott
Chamberlain a ?crit :
Hi Marten,
The test I referred to tests for similarity of topology
only, ignoring
branch lengths. On the website made by de Vienne
et al. you can input two
newick trees and the site calculates
the Icong index, which determines
how similar the topologies
are, and gives you a p-value. I use it in the
context of trying
to argue that a tree I have made is *similar enough* to
a
published tree of the same group of organisms. I believe you have to
delete all unshared taxa between the two trees you input.
I am interested purely in the trees, not community
ecology data, so
phylosor and NRI are not applicable in this
case.
Scott
On Tuesday, January
18, 2011 at 12:34 PM, Marten Winter wrote:
Dear Scott,
do you
really want to test for similarity of the shape of the trees? If
yes please let me know how to do this :O)
If you would also be satisfied with a similarity based on the
shared
branches I suggest something like Phylosor or may be
NRI...
cheers, Marten
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