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 <[email protected]> Subject: Re: [Biojava-l] Simple Question - Creating a Java object (some form of Tree) from a Newick format file To: JP <[email protected]> Cc: [email protected] Message-ID: <1245434175.8158.6.ca...@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/[email protected]/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 - [email protected] > 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: [email protected] http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
