Hi all,
To complete this discussion, the package distory computes Billera et
al.'s geodesic distance between two trees.
Cheers,
Emmanuel
Scott Chamberlain wrote on 04/03/2011 00:44:
There is also SH.test (Shimodaira-Hasegawa test) in package phangorn
And the Icong index by de Vienne which only compares topology (See this
website: http://www.ese.u-psud.fr/utilisateurs/devienne/index.html)
-Scott
On Thursday, March 3, 2011 at 11:37 AM, John Cumbers wrote:
Hi Alastair,
See these functions below, dist.topo is in library(Ape)
Cheers,
John
# check for similarity
# do the two trees produced by MrBayes and raxML have the same topology?
all.equal(tree1, tree2, use.edge.length = FALSE)
# result = TRUE or FALSE.
# calculate the distance between the two tree, using default method. ( Penny
and HardyÂ’s 1985)
dist.topo(tree1, tree2)
# result = numeric measure of distance
On Wed, Mar 2, 2011 at 11:25 PM, Alastair Potts <pott...@gmail.com> wrote:
Good day all,
I was wondering if there is a tree statistic that compares the topology of
two trees which gives and indication of the degree of similarity or
dissimilarity between the trees?
Cheers,
Alastair
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Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
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