Hello Andy, As far as I know there is no support for the phyloXML format in R yet. There might be better ways of doing it and I'd love to hear about them but what I did was to use archeopteryx: http://phylosoft.org/archaeopteryx/
and then go in File > Read tree from Tree of Life, enter the node identifier and save the tree in the Nexus/Newick format so that you can load it in R with ape or phylobase. Cheers, -- François On Thu, 2010-11-04 at 19:41 -0300, Andy Rominger wrote: > Dear list, > > Has anybody come across a way to read-in a tree in the "ToL Response Format" > or in treeML format--both XML formats? I should be more specific: by > read-in I mean convert into some useful R class (e.g. ape's phylo). Forgive > me if I have missed an obvious function in one of the many packages. > > Here are two example outputs that I would like to be able to use: > ToL Response Format > http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id=26391&optype=0 > > treeML > http://tolweb.org/onlinecontributors/app?service=external&page=xml/TreeStructureService&node_id=26391&optype=1 > > If no function exists, I could imagine using scan() and then somehow > converting the XML to a Newick format, or perhaps an "edge" matrix as used > by phylo? There is probably a more elegant method! > > All suggestions are most appreciated! Thanks for the help-- > Andy Rominger > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
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