Re: [R] Package for phylogenetic tree analyses

From: Ramon Diaz-Uriarte <rdiaz02_at_gmail.com>
Date: Sat 27 Jan 2007 - 10:21:40 GMT

Dear Lalitha,

On 1/26/07, lalitha viswanath <lalithaviswanath@yahoo.com> wrote:
> Hi
> I am looking for a package that
> 1. reads in a phylogenetic tree in NEXUS format
> 2. given two members/nodes on the tree, can return the
> distance between the two using the tree.
>
> I came across the following packages on CRAN
> ouch, ape, apTreeShape, phylgr all of which seem to
> provide extensive range of functions for reading in a
> Nexus-format tree and performing phylogenetic
> analyses, tree comparisons etc, but none to the best
> of my undestanding seem to provide a function obtain
> distances (in terms of branch lengths) between two
> nodes on a single tree.
> I am working with just one tree and need a function to
> return distances between various pairs of nodes on the
> tree.
>
> Is there any other package out there that has this
> functionality?

I've been away from that area for some years now, but certainly our phylogr package will not do what you want. However, I think there are various external (non R) programs that will do it, and that might be all you need if this is just a sporadic use. The set of programs distributed and maintained by Ted Garland (PDAP) did provide the type of output you want (in the form of a matrix of distances). I am sure there are others out there (I bet PHYLIP does it too).

HTH, R.

>
> Thanks for your responses to my earlier queries. As a
> beginning R programmer, your responses have been of
> utmost help and guidance.
>
> Lalitha
>
>
>
> ____________________________________________________________________________________
>
> Access over 1 million songs.
>
> ______________________________________________
> R-help@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
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz

______________________________________________
R-help@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
and provide commented, minimal, self-contained, reproducible code.
Received on Sat Jan 27 21:24:22 2007

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.1.8, at Sat 27 Jan 2007 - 11:30:30 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.