[Bioperl-l] Parsing Newick format

Jason Stajich jason@cgt.mc.duke.edu
Fri, 15 Nov 2002 10:14:20 -0500 (EST)

On Fri, 15 Nov 2002, Serena Fritsch wrote:

> Hello. we have a question concerning parsing the newick-format in
> Perl. We want to parse a newick tree and transform it into an internal
> hierarchical data structure (like a n-ary search tree). Does something
> like this already exist with bioperl?

That's what you get when you parse in the file and get back a
Bio::Tree::Tree object.

The node object has methods for children and parents of each node so you
can walk up and down the tree.  Look at the interface Bio::Tree::TreeI and
Bio::Tree::NodeI as starting points - let us know if you have specific
needs that aren't met.  Quite a lot of work has gone on with these classes
since 1.0 (and there are bugs in it for 1.0.2) so you may want to venture
into getting the latest version from CVS if you want to try and develop
off these.

Also, we'd love to see new functionality if you've got ideas or end up
using the trees in a specific way.


> Thank you very much in advance!
> Serena and Michael
> ________________________________________________________________
> Viren? Wir wissen nicht was Ihr Arzt empfiehlt. Wir empfehlen den
> Virencheck für Dateianhänge! http://freemail.web.de/features/?mc=021159
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l

Jason Stajich
Duke University
jason at cgt.mc.duke.edu