[pyphy] [Fwd: phylogenetic python]

Tue, 29 Jun 1999 15:31:57 +0000

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This message came from Jeffrey Chang at Stanford...Jeff
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Date: Tue, 29 Jun 1999 00:06:33 -0700 (PDT)
From: Jeffrey Chang <jefftc@leland.Stanford.EDU>
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To: jeff@theopenlab.uml.edu
cc: Rick Ree <rree@oeb.harvard.edu>
Subject: Re: phylogenetic python
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Hi Jeff,

I have recently received an email from you colleague Rick Ree alerting me
to your efforts with Open Lab.  I have visited the web site and agree with
the principles of the group.  It's definitely frustrating to have to
redevelop code that I just *know* someone else must have done before.

My main research area is in bioinformatics, so I do not do a lot of
software development for phylogenetic analysis, per se.  However, I do
have a recursive descent parser for Phylip rooted trees and a cladogram
viewer for Tk.  All the code is in python.

I will be happy to make those modules available to you under a license
like Python's (pretty unrestrictive), if you think they would be helpful. 

Jeff

On Fri, 25 Jun 1999, Rick Ree wrote:

> Hi, I just happened to run across your post to the Python newsgroup, and
> noticed your mention of a phylogenetic tree viewer in Python.
> 
> There is a small phylogenetic Python development effort going on at the
> OpenLab (http://theopenlab.uml.edu), which is a consortium of biology
> types who are interested in free (open-source) software.  Currently, there
> are PyGnome- and Tkinter-based phylogeny editors that are being being
> developed, that share a common code base (just different GUI code).  I
> initiated and am developing the PyGnome version, which is called Mavric.
> The Tkinter version is called Herring.
> 
> Currently, Mavric can read and write Newick-formatted trees, and features
> click-and-drag brach swapping, branch pruning, collapsing, rotating, and
> more.  The aim is to provide the convenience of MacClade and more, plus
> the added bonus of ease of development using Python, and an open source
> model of development.  Herring offers Postscript printing of trees as
> well. 
> 
> I've also written some quick and dirty python code for reading/writing
> Phylip files, and very limited Nexus support.  It would be nice to get
> more functionality on this end also.
> 
> Would you be interested in contributing to the project?  The coordinator
> of the OpenLab is another Jeff: jeff@theopenlab.uml.edu.  He is extremely
> nice, energetic, and will give you a CVS account if you want to check out
> Mavric or Herring.  I am just about to leave the country for three months,
> so you should contact him if you are interested in checking it out.
> 
> Are you in Ackerly's lab?  If so, say hi for me!  Anyway, I hope that this
> is interesting to you and that you might want to contribute.
> 
> --Rick Ree
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Harvard University Herbaria           | (617) 496-3374 (v) 495-9484 (f)
> 22 Divinity Ave., Cambridge, MA 02138 | www.herbaria.harvard.edu/~rree
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> 

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