[R] Package for phylogenetic tree analyses

[Ramon Diaz-Uriarte]

Dear Lalitha,

On 1/26/07, lalitha viswanath <lalithaviswanath at 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
>
>
>
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-- 
Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz