[Phylobase-devl] Phylobase GSoC idea

[Brian O'Meara]

On Mar 10, 2008, at 9:29 PM, Steve Kembel wrote:

>
>> Brian did mention that there were some existing C++ libraries
>> for tree manipulation etc. ... patching into these might be
>> the (an?) answer?
>
> I rewrote the idea I proposed before to open it up to a wider range of
> potential projects, from tree manipulation to multi-tree, metadata or
> even buildiing an interface with nexml or nexus (i.e. more work on the
> ioNCL code). See below. Too vague now?

Just a note about the C++ libraries: the one I've used is Rod Page's  
Treelib, which allows uppass/downpass moves and the like, but might  
not be better than what's already in R. A student at a course I'm  
involved with today mentioned Bio++, which seems little-used but is  
actually updated and can, according to its documentation, do parsimony  
and likelihood analyses, get consensus trees, reroot trees, and the  
like. There's some info at http://home.gna.org/bppsuite/ and a  
Bioinformatics note at http://www.biomedcentral.com/1471-2105/7/188 .

Brian