Hi, 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 contribute. Nicholas On Thu, 11 Sep 2003 09:21:56 -0700 (PDT), "Susan Holmes" <susan@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@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > >