[R] Package for phylogenetic tree analyses
rdiaz02 at gmail.com
Sat Jan 27 11:21:40 CET 2007
On 1/26/07, lalitha viswanath <lalithaviswanath at yahoo.com> wrote:
> 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
> Is there any other package out there that has this
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).
> Thanks for your responses to my earlier queries. As a
> beginning R programmer, your responses have been of
> utmost help and guidance.
> Access over 1 million songs.
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Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
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