Thomas- I think your interests might be served by my function expandTaxonTree in my library paleotree on CRAN. Given a genus-level tree with data on the species within each genus, it will turn each genus into an unresolved polytomy of the congeneric species. -Dave
On Tue, Oct 2, 2012 at 3:08 AM, Davies, Thomas <thomas.dav...@exeter.ac.uk> wrote: > Dear All > > Sorry to mass email with what could be a very basic question. I am trying to > generate a tree for 1000 plus species. To reduce the search effort I first > generated a tree to genus level from NCBI Itol with the intention of adding > species branches to each genus after. Doing this manually has invariably > proved challenging as it's difficult to locate and solve all the sources of > human error that creep in when manual editing. Is there a function in R that > can do this? Say something that matches the genus in the species name to the > genus tip on the tree, and adds branches accordingly? It is not my intention > that the tree be based on divergence times, this isn't feasible given the > number and order of species I am working with, hence the reason for using the > NCBI taxonomy. > > Any help is much appreciated > > cheers > > Tom > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ http://cran.r-project.org/web/packages/paleotree/index.html _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
