[Biopython-dev] [Wg-phyloinformatics] GSoC Weekly Update 11: PhyloXML for Biopython

[Peter]

On Wed, Aug 5, 2009 at 11:31 PM, Eric Talevich<eric.talevich at gmail.com> wrote:

> OK, it works now but the resulting trees look a little odd. The options
> needed to get a reasonable tree representation are fiddly, so I made
> draw_graphviz() a separate function that basically just handles the RTFM
> work (not trivial), while the graph export still happens in to_networkx().
>
> Here are a few recipes and a taste of each dish. The matplotlib engine seems
> usable for interactive exploration, albeit cluttered -- I can't hide the
> internal clade identifiers since graphviz needs unique labels, though maybe
> I could make them less prominent. ...

Graphviv does need unique names, and the node labels default to the
node name - but you can override this and use a blank label if you want.
How are you calling Graphviz? There are several Python wrappers out
there, or you could just write a dot file directly and call the graphviz
command line tools.

Peter