Hi Silvan - I'd love to proven wrong, but I think unless
you're interested in a cluster dendrogram
(neighbour-joining or UPGMA etc.) that the most standard
phylogeny-generation algorithms aren't implemented as R
functions (yet). There are very efficient third party
programs for tree construction (PAUP* at
http://paup.csit.fsu.edu is the default, PHYLIP at
http://evolution.genetics.washington.edu/phylip.html is
99% as comprehensive, and free) and the ape package
provides a way of getting your trees and data into R for
any further analysis you want.
Regards,
Rich
On Mon, 3 Jan 2005 18:15:44 +0200
"Sivan Aldor" <sivana1 at techunix.technion.ac.il>
wrote:>Hello,
>My name is Sivan and I am a master degree student in
>statistics,my problem is as follows:
>I have a dataset containing gene sequences and I would
>like to create a phylogenetic tree from it.
>The problem that I can't seem to find a function to do
>this kind of operation. I read the ape package manual and
>I haven't found a command that takes raw data and turns
>it into a tree.
>does anyone know if such a command exist?
>thank you in advance,
>sivan
> [[alternative HTML version deleted]]
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-------------------------------
Rich Grenyer, Ph.D.
Postdoctoral Research Associate
Biology Department - University of Virginia
Charlottesville, VA 22904
USA
Tel: +1-434-982-5629 Fax: +1-434-982-5626
email: grenyerDELETE at virginia.edu