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
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
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--
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
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