A recent paper published in Cladistics provides a phylogeny of 73060 (yes, seventy three thousand and sixty) taxa representing most of the known eucaryotic groups. The tree can be downloaded as supplementary materials, but I have to say that the trees are provided in TNT format and that I was unable to format the trees for input in other programs because Vim tilted sistematically (I didn't tried to much anyway, so I think that someone with patient and a real need to use the tree, mine was only curiosity, could do it). This is the reference: Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups (p 211-230) Pablo A. Goloboff, Santiago A. Catalano, J. Marcos Mirande, Claudia A. Szumik, J. Salvador Arias, Mari Källersjö, James S. Farris. Cladistics Volume 25 Issue 3.
Enjoy! Leandro Jones http://www.efpu.org.ar 2009/8/20 Brian O'Meara <[email protected]>: > There's not yet a good single source. TreeBase.org has some topologies, but > not all studies go in there yet. The largest one I know of there has 1569 > taxa . The PhyLoTA browser (<http://loco.biosci.arizona.edu/pb/>) has trees > for many groups and also allows you to download aligned data to make your > own. You can download NCBI's taxonomy, which is a sort of tree, though not > highly-resolved or with branch lengths, but at least pretty comprehensive. > You can also download the tree used by the Tree of Life project > (<http://tolweb.org/tree/home.pages/downloadtree.html>). There may be a tree > available from <http://www.timetree.org/>, but I haven't been able to find > it in a form other than a pdf image. > > Having a place to download the single best current estimate of the full tree > of life would be great, and there are a few research groups working towards > this goal, but it's not ready yet, as far as I know. > > Hope this helps, > Brian > > ________________________________________________ > Brian C. O'Meara > Asst. Prof., Dept. of Ecology and Evolutionary Biology > University of Tennessee, Knoxville > http://www.brianomeara.info > 865-408-TREE (8733) > > > On Aug 20, 2009, at 7:31 AM, saikari keitele wrote: > >> Hi, >> >> >> >> I'm trying to use the picante r package. >> >> My aim is to use it to construct phylogenetic trees and calculate >> diversity >> statistics from species occurrence data in different geographic regions. >> >> So, I have a list of species names with abundance information (number of >> occurrences) and would like to use Phylomatic to construct a tree. >> >> The Phylomatic documentation mentions that a reference tree is needed and >> different examples of megatrees ( >> http://svn.phylodiversity.net/tot/megatrees/) are given for this. However, >> they apply only (I think) to trees and plants. My data includes other >> kinds >> of organisms. Do you know of any other downloadable reference trees that >> include the whole taxonomy? >> >> >> >> Thank you very much. >> >> >> >> Saikari >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-phylo mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > _______________________________________________ > R-sig-phylo mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- Leandro R. Jones, Ph.D. http://www.efpu.org.ar "... To use a computer implies abandoning all techniques developed before to the advent of automated calculation, I say techniques, not sciences..." (J. P. Benzecri) _______________________________________________ R-sig-phylo mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
