Re: [R-sig-phylo] Phylogenetic reference trees

Thank you very much for all your helpful replies. Thanks also for giving me the link of Tree of Life, and the link to the Cladistics paper. I had thought about using NCBI's taxonomy or species 2000 taxonomy (http://www.sp2000.org/), but I had believed -maybe mistakenly, I'm pretty illiterate in bi

Re: [R-sig-phylo] Phylogenetic reference trees

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 unabl

Re: [R-sig-phylo] Phylogenetic reference trees

You can also "tinker" your own tree with the help of Phylomatic and the APweb Tree behind it () as I have done it for ca. 12700 species. It was a major task but it worked (but only for plants). cheers, M. Brian O'Meara schrieb: There's not yet a g

Re: [R-sig-phylo] Phylogenetic reference trees

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 () has trees for many groups and also allows you to download aligned data to m

[R-sig-phylo] Phylogenetic reference trees

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 li