[Biojava-l] Newick Tree Visualization

[Tiago Antão]

Hi,

I am new to this list, but I am actually also doing phylogenetic tree
visualization and I have been using JGraph/JGraphT with some success.

A very simple start can be seen here:
http://www.jgrapht.org/visualizations.html

I have code that I can share, but it is not really in Java, but in
clojure (a Lisp running on the JVM). But, if anyone is interested,
just say.

Tiago
On Fri, Oct 30, 2009 at 4:49 PM, Marc Colosimo <mcolosimo at mitre.org> wrote:
>
> Mara,
>
> Or TreeViewJ <http://treeviewj.sourceforge.net/Site/TreeViewJ.html> which
> handles PhyloXML, nwk and extended nwk. It also has a light weight library
> that does some of the things found in PAL (found in  subversion source).
>
> Marc
> On Oct 30, 2009, at 12:00 PM, biojava-l-request at lists.open-bio.org wrote:
>>
>> Date: Fri, 30 Oct 2009 11:00:02 -0400
>> From: Hilmar Lapp <hlapp at gmx.net>
>> Subject: Re: [Biojava-l] Newick Tree Visualization
>> To: Mara Axiom <mara.axiom at gmail.com>
>> Cc: biojava-l at lists.open-bio.org
>> Message-ID: <CBF42F90-076C-484C-A450-C5DCCD137727 at gmx.net>
>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>>
>> Mara - have you looked at PhyloWidget? (http://www.phylowidget.org)
>>
>>        -hilmar
>>
>> On Oct 30, 2009, at 10:34 AM, Mara Axiom wrote:
>>
>>> Hello,
>>>
>>> I'm new to BioJava. I have copied the code "*getTreeAsJGraphT
>>> (Weighted
>>> Tree)*" from http://biojava.org/wiki/BioJava:PhyloSOC07_doc which
>>> basically
>>> parses a Newick string, and displays the result in text using
>>> JGraphT. It
>>> works! My question is how to visualize the result in form of a
>>> graphic tree,
>>> not text? Is there any way to do this in BioJava? Is there any
>>> source code
>>> or example that can help me? Any help is appreciated.
>>>
>>> I was looking at JGraph, but I'm not sure if it does what I want. If
>>> it
>>> does, I don't know where to start.
>>>
>>> Mara
>>>
>>> P.S. I know there are tools which do this, but I need to create my
>>> own code
>>> for something specific I want.
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>
>
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