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

Colosimo, Marc E. mcolosimo at mitre.org
Mon Jun 22 13:19:01 UTC 2009

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. 


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:



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
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Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com

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