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Newick Tree Visualization
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Newick Tree Visualization
by Mara Axiom
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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@... http://lists.open-bio.org/mailman/listinfo/biojava-l |
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Re: Newick Tree Visualization
by Hilmar Lapp
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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@... > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== _______________________________________________ Biojava-l mailing list - Biojava-l@... http://lists.open-bio.org/mailman/listinfo/biojava-l |
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Re: Newick Tree Visualization
by Tiago Antão
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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@...> 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@... wrote: >> >> Date: Fri, 30 Oct 2009 11:00:02 -0400 >> From: Hilmar Lapp <hlapp@...> >> Subject: Re: [Biojava-l] Newick Tree Visualization >> To: Mara Axiom <mara.axiom@...> >> Cc: biojava-l@... >> Message-ID: <CBF42F90-076C-484C-A450-C5DCCD137727@...> >> 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@... >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> >> > > _______________________________________________ > Biojava-l mailing list - Biojava-l@... > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- "The hottest places in hell are reserved for those who, in times of moral crisis, maintain a neutrality." - Dante _______________________________________________ Biojava-l mailing list - Biojava-l@... http://lists.open-bio.org/mailman/listinfo/biojava-l |
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