Dear Lalitha, On 1/26/07, lalitha viswanath <[EMAIL PROTECTED]> 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. > > ______________________________________________ > [email protected] 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 ______________________________________________ [email protected] 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.
