[Bioperl-l] display Newick trees

Jason Stajich jason at cgt.duhs.duke.edu
Tue Jul 27 17:21:36 EDT 2004

On Tue, 27 Jul 2004, Arlin Stoltzfus wrote:

> On Friday, July 16, 2004, at 12:24 AM, dimka wrote:
> > I'm looking for a perl program that would generate evolutionary trees
> > (ps, png, gif) read from a Newick (phylip dnd) file,
> > http://evolution.genetics.washington.edu/phylip/newicktree.html
> We have some Perl software called nexplot that we developed for our own
> purposes that may be of use.  It is not a part of BioPerl, yet.  You can
> test out the functionality at www.molevol.org/nexplorer, and from there
> you can download the Perl library and applications to make PostScript
> plots of trees.  Nexplot uses a NEXUS files as input, and outputs a tree
> with the tips aligned with a data matrix (e.g., a sequence alignment).
> However, it has a tree-only mode, and the NEXUS input file incorporates
> the Newick standard tree format in its TREES block, so it would be easy
> (in principle) for you to just create NEXUS files with the trees you
> want to display, and then use nexplot to display them (you can even put
> multiple named trees in a single file, and nexplot can plot a tree
> chosen by name).

And I've just added last week write_tree capabilities to
Bio::TreeIO::nexus so it is even easier to generate the input files to

It may need a little more testing but worked great for my needs.


> Arlin
> ------------------
> Arlin Stoltzfus (arlin.stoltzfus at nist.gov)
>    Research Biologist, NIST; Adj. Asst. Prof., UMBI
> CARB, 9600 Gudelsky Drive, Rockville, Maryland  20850
> tel 301 738 6208, fax 301 738 6255, web home www.molevol.org/camel
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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