[BioC] R and ARB

A.J. Rossini rossini at blindglobe.net
Thu Sep 11 08:55:17 MEST 2003

"Nicholas Lewin-Koh" <nikko at hailmail.net> writes:

> 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 :)

I'd avoid phylip, since commercial institutions might not be able to
use it (Joe F has a really strange license on it).

See the "ape" package in CRAN which does some of this stuff as well...


A.J. Rossini     			
rossini at u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
UW   :              FAX=206-543-3461 | moving soon to a permanent office
FHCRC: 206-667-7025 FAX=206-667-4812 | Voicemail is pretty sketchy/use Email

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