[Bioperl-l] display Newick trees

Arlin Stoltzfus stoltzfu at umbi.umd.edu
Tue Jul 27 11:23:07 EDT 2004

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 
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 
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 
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 
by name).


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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