[Bioperl-l] Capabilities of Bio::Tree

[Jason Stajich]

On Thu, 20 Nov 2003, Bryony Mackenzie wrote:

> Hello,
>
> I am interested in using the Bio::Tree module and would like to read in
> Newick format and convert to a web-friendly
> graphical format. Ideally I want to use colours and other options to
> prettify the tree.
>
> I have looked at using the Treeplot program but it does not seem to
> distinguish properly between my consensus trees
> with bootstrap values and trees with branch lengths. It tries to
> interpret my boostraps as branch lengths :(

I have had no problems with treeplot, are you sure you are putting the
labels on correctly?

My tree looks like this

 ((a:1,b:1)75:2,c:3);

and I get a bootstrap value of 75 labeled for the a,b clade.

Are you having trouble with trees that are converted to-from the bioperl
tree reading and then to treeplot?

As for colors, etc, that is also possible with treeplot
http://www.cnrs-gif.fr/pge/bioinfo/treeplot/index.php?lang=en#ancre_exemples
does it not work for you?

If someone wanted to work on a wrapper for Treeplot in Bioperl this would
be very helpful.

> I have read the docs but am still confused as to the abilities of
> Bio::Tree. I see that handling phylogenetic trees has been
> put down as a problem area for bioperl and I was wondering what progress
> is being made ?

We currently don't support tree drawing natively in bioperl - you must use
a 3rd party application.  Seems like a interesting problem for someone to
work on.  Allen Day has some sort of SVG tree plotting output as well but
not sure how primetime that is.

As for the current capabilities - do you want a list of all the supported
functionality or are you angling for something in particular other than
the drawing part?

I'm currently working on implementing some more statistics, random tree
generation, distance calculations, and some topology comparison stuff.
So in short - not much on the automated pretty output front so we
definitely need people helping out there.

> Thanks,
> Bryony
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu