[BioPython] Phylogenetics trees

[Jeffrey Chang]

I don't see any reason to move the Mavric project into biopython.  As far
as I know, it's fine where it is.

However, I believe that Rick was offering to help implement classes in
biopython that could work on phylogeny trees?  Perhaps Greg and Rick could
build underlying infrastructure-type stuff in biopython, that could be
used by both Mavric and Greg's GUI.

Jeff




On Wed, 30 Aug 2000, Rick Ree wrote:

> Regarding the licensing differences between mavric and biopython, IANAL
> either :)  I would like to keep mavric under the GPL though (no flames
> please!)  So maybe the best thing to do is keep mavric separate from the
> biopython distribution, but let biopython users know it is available--
> maybe a link to it on the 'Related' page of the website?
> 
> If anyone has suggestions of ways in which mavric could be developed to
> work better with biopython, please let me know. 
> 
> --Rick
> 
> On Tue, 29 Aug 2000, Andrew Dalke wrote:
> 
> > There is a licensing difference between Mavric and biopython.  Mavric
> > is distributed under the GNU GPL while biopython uses the Python license,
> > "with the serial numbers scratched off."  It's basically the same as
> > the modified BSD license.
> > 
> > The GPL says:
> > > But when you distribute the same sections as part of a whole which is
> > > a work based on the Program, the distribution of the whole must be on
> > > the terms of this License, whose permissions for other licensees extend
> > > to the entire whole, and thus to each and every part regardless of who
> > > wrote it.
> > 
> > I want my contributions to stay BSD-like, or rather, want some way for
> > people to use my contributions under a BSD-like license.  That clause
> > of the GPL means that if Mavric code is added to biopython then any
> > of my work included in a biopython distribution must also be licensed
> > under the GPL.
> > 
> > Whether or not my contributions are then available under both the
> > current license and the GPL or only the GPL, I'm not enough of an lawyer
> > to say.  (That is, can someone get the biopython distribution, pull
> > out the Mavric parts and use only the BSD-like license on the rest?
> > Probably, if the copyright is owned by me.  Probably not if anyone made
> > any changes under the expectation that the changes were under the GPL.)
> > 
> > That means I will need some other way to distribute my software, which
> > is a distinct negative point - two code bases, or some way to extract
> > one part from the other, including notifying people about the differences
> > in the parts they are modifying.
> > 
> > Therefore I argue against including Mavric code in biopython unless the
> > inclusion is made under a more lenient license, like the LGPL.
> > (Lenient in this case means accepting of non-GPL software.)
> > 
> > I suppose this might end up in a yet another licensing flame war (*sigh*)
> > so I'll just point to http://www.linux.com/news/articles.phtml?aid=7125
> > for a description and leave it at that.
> 
> 
> 
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