[BioC] R and ARB

Susan Holmes susan at miller.stanford.edu
Thu Sep 11 10:21:56 MEST 2003

You can also look into trexml
which does use Felsensteins' program, I don't think you have to worry
about keeping away from Felsenstein's code, his copyright notice
is pretty clear, he doesn't want others to use it and then sell
their software, as detailed also on marty Wolf's trexml page.

I think it would be most useful to have a ml implementation in R,
we are developping packages that compute distances between trees
as they are output by phylip (in Newick format),
we have developed our own treeclass for this,
I have also developed various other interfaces to phylip,
but would actually like a more ``R-based'' approach
(ape does not do any tree estimation either).

Please make more precise what kind of help you would like,
I would be all for using trexml, what do you think.
Susan Holmes
Statistics, Stanford

On Thu, 11 Sep 2003, Nicholas Lewin-Koh wrote:

> Hi,
> I have a package in development for fitting additive tree models to data.
> Basically the core of the package is and R interface to TRex, Vladimir
> Makarenkov has givien me permission to release this on CRAN or
> Bioconductor under gpl. Besides the TRex functions for least squares
> fitting of trees and reticulograms, I am adding functions for plotting,
> rooting trees, a tree class that extends the graph class and some more
> general stuff for additive trees were one has replicate distance matrices
> as often occurs in psychology. I would like to add tools for maximum
> likelihood estimation, but I am not sure of the phyllip license and I
> don't want to appropriate code if it is not kosher. I am still working on
> some of the tree display algorithms which is going slow since I hold a
> job in the day that is not opensource friendly.
> If anyone is interested in codeveloping I am happy to share the load :)
> Nicholas
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