[R-sig-phylo] Phylogenetic reference trees
bomeara at utk.edu
Thu Aug 20 15:18:30 CEST 2009
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 C. O'Meara
Asst. Prof., Dept. of Ecology and Evolutionary Biology
University of Tennessee, Knoxville
On Aug 20, 2009, at 7:31 AM, saikari keitele wrote:
> I'm trying to use the picante r package.
> My aim is to use it to construct phylogenetic trees and calculate
> statistics from species occurrence data in different geographic
> 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.
> 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
> include the whole taxonomy?
> Thank you very much.
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