[BioC] R and ARB

Nicholas Lewin-Koh nikko at hailmail.net
Fri Sep 12 01:54:20 MEST 2003

Just took a quick look at the code and it doesn't llok like it would be
too difficult to port since it is a command line interface. I don't have
a problem using it, though I will email the authors and see about getting
"better" license on it. Better meaning something more established with
better legal ramifications such as the mit license. Licensing is a pain
but it is important to respect the copyright and intent of the authors.

I agree about having an R interface to the phylogenetic estimation
routines. Especially as Bioconductor gets better sequence processing
facilities. I would be happy to include some of your implementations in
the package and work you guys in as co-authors if you would like to


On Thu, 11 Sep 2003 09:21:56 -0700 (PDT), "Susan Holmes"
<susan at miller.Stanford.EDU> said:
> Nicholas,
> You can also look into trexml
> http://jcsmr.anu.edu.au/dicb/humgen/marty/trexml/trexml.man.html
> 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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> >

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