[Bioperl-l] Re: Bioperl tree class

Malay curiouser@ccmb.ap.nic.in
Fri, 12 Oct 2001 12:04:05 -0700 (PDT)

On Wed, 10 Oct 2001, Richard Copley wrote:

> >>Did you (or anyone else) get around to writing a bioperl object that can
> >>read in PHYLIP format tree files? I am on the verge of writing one; it
> >>wouldn't take long, but there's no sense duplicating effort.
> >>
> > 
> > No, I haven't, neither has my group in Singapore, just mailing bioperl, to
> > check if Jason or others are working on it.
> I started writing one ages ago but didn't finish - I attach it on the off 
> chance it's useful - realistically, it would take a lot of work. This uses 
> recursion - not sure if this is the best way to do it. I also put in a 
> function for drawing the tree using GD. Again this works in a limited fashion 
> but is far from a production product.
> The one thing I want to plead for any bioperl Tree class is that any 
> implementation can deal with multifurcating trees. (Does that make them graphs?).
I am really interested in Tree module. Will be nice to have the graphics
generated through my BioSVG module.

Malay Kumar Basu 
Centre for Cellular and Molecular Biology 
Hyderabad 500007 

Fax: (00-91)40-7171195  Phone: (00-91)40-7172241