[BioPython] Phylogenetics trees

[Jeffrey Chang]

On Wed, 30 Aug 2000, Jeffrey Chang wrote:

> 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.

Oops, except for the dang license issue...


> 
> 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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> > http://biopython.org/mailman/listinfo/biopython
> > 
> 
> 
> 
>