[pyphy] Re: phylogenetic python

[Jeffrey Chang]

Hi Jeff,

I'm trying to put together a paper for PSB due next week.  I will write
you next week to see about contributing code!

Thanks,
Jeff


On Tue, 29 Jun 1999, J.W. Bizzaro wrote:

> 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/
> --
>