[Biojava-l] Simple Question - Creating a Java object

[Colosimo, Marc E.]

If you just want to view a tree, try TreeViewJ <http://sourceforge.net/projects/treeviewj/>. The GUI can read in newick and phyloXML trees and import trees from Nexus files. It can export back out to newick and phyloXML or as SVG or JPEG images. I have more code that I'll be checking in soon. 

Best,
Marc


From: Richard Holland <holland at eaglegenomics.com>
Subject: Re: [Biojava-l] Simple Question - Creating a Java object
	(some form of Tree) from a Newick format file
To: JP <jp at javaclass.co.uk>
Cc: biojava-l at biojava.org
Message-ID: <1245434175.8158.6.camel at buzzybee>
Content-Type: text/plain

Biojava has a parser which understands Nexus files, including the
embedded Newick tree data. You could probably extract and modify the
Newick bits to run standalone. The Nexus code is written up here:

http://biojava.org/wiki/BioJava:PhyloSOC07_doc
http://www.biojava.org/docs/api/org/biojavax/bio/phylo/io/nexus/package-summary.html
http://www.mail-archive.com/biojava-l@lists.open-bio.org/msg00892.html

cheers,
Richard


On Fri, 2009-06-19 at 18:37 +0100, JP wrote:
> Does anyone know of a tool to create a tree by parsing a Newick Tree format
> file in Java ?
> Is there anything in biojava to read this ?
> 
> Many Thanks
> JP
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
-- 
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
http://www.eaglegenomics.com/