[pyphy] Re: phylogenetic python

[J.W. Bizzaro]

Hi Jeffrey!

Or do you prefer Jeff?

Some history: The two coordinators of the PyPhy project at The Open Lab are
Thomas Sicheritz and Rick Ree.  Mavric was Rick's personal project before he
moved development to TOL.  He maintains this Web page for it:

    http://theopenlab.uml.edu/mavric/mavric.html

Thomas, who lives in Sweden and started helping with The Loci Project...

    http://theopenlab.uml.edu/loci/

is now turning his attention to a phylogenetics project.  He used to work in
Tcl/Tk and wrote a bioinformatics module (BioWish) in that language.  But now
he's going to give Python a shot, so he got together with Rick to start the
PyPhy project:

    http://theopenlab.uml.edu/pyphy/

The exact relationship between Mavric and PyPhy is something even I'm not
totally clear on, but I think Mavric (and Herring - like Mavric with Tkinter)
falls under PyPhy in general.

If you are interested in helping Rick and Thomas, you should at least join the
mailing list:

    http://theopenlab.uml.edu/mailman/listinfo/pyphy/

If you will be contributing code, which I guess you are, I can give you a shell
account (username jeff is taken ;-) and access to the CVS server.

Regarding specifics like licensing, it is really up to Thomas and Rick, since
they're the project coordinators (I coordinate Loci in addition to TOL, but not
PyPhy).  But any license less "restrictive" than the GNU GPL should work.  If
the license is like Python's, which is almost freeware, there shouldn't be a
problem.  (We really prefer the GNU licenses, especially for whole projects,
since it is best able to keep source code free, "as in free speech".)

This message is also being sent to the PyPhy list.  Rick is away, but Thomas
should respond.  As soon as I get some word about how you want to coordinate
things, I'll give you an account.


Cheers.
Jeff


Jeffrey Chang wrote:
> 
> 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
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >
> >
> >

-- 
J.W. Bizzaro                  mailto:bizzaro@bc.edu
Boston College Chemistry      http://www.uml.edu/Dept/Chem/Bizzaro/
--