[R] building phylogenetic trees

[Rich Grenyer]

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]]
>
>______________________________________________
>R-help at stat.math.ethz.ch mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide! 
>http://www.R-project.org/posting-guide.html

-------------------------------
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