Not sure if I understand the problem completely, but this should allow you to
examine all of the clades (and should work if polytomies are involved):
# for tree phy
rootID <- length(phy$tip.label) + 1;
for (i in rootID:max(phy$edge[,1])) {
clade <- extract.clade(phy, i);
# do something
}
This includes the root node (i.e. whole tree), but that can be changed. This
can be rewritten as an lapply if necessary.
HTH.
JWB
________________________________________
Joseph W. Brown
Post-doctoral Researcher, Smith Laboratory
University of Michigan
Department of Ecology & Evolutionary Biology
Room 2071, Kraus Natural Sciences Building
Ann Arbor MI 48109-1079
josep...@umich.edu
> On 5 Jan, 2017, at 15:50, Kamila Naxerova <knaxer...@partners.org> wrote:
>
> Hi all,
>
> I would like to break a phylogenetic tree into all possible clades and then
> examine each one of them for certain characteristics.
>
> I am writing some code to do this from scratch, but it’s getting pretty
> cumbersome quickly.
>
> I was wondering whether there are some functions out there already that could
> help me with this task?
>
> Thanks so much for any help.
>
> Cheers,
> Kamila
>
>
> The information in this e-mail is intended only for th...{{dropped:21}}
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