[BioPython] Phylogenetics trees

[Rick Ree]

On 30 Aug 2000, Brad Chapman wrote:

> I guess when I was thinking about things, I was thinking something like
> Jeff suggested -- to implement general classes that work on phylogeny
> trees. I think this type of code would be useful for multiple projects
> (ie. Mavric and Greg's tk viewer project) and it wouldn't really be
> necessary to absorb the projects into the BioPython distribution.
> 
> Rick, what do you think about trying to make the Mavric tree
> manipulation libraries fit into the Biopython distribution? As far as
> licensing goes, you could have the libraries be under the less
> restrictive Biopython license, and then retain Mavric (as a separate
> package) under the GPL by making all of the Mavric-specific code
> licensed under the GPL. This is of course completely up to you, but
> might satisfy the goals of making this type of code available to other
> people who would like to use it for their projects (ie. Greg) and also
> keeping Mavric a stand-alone entity. 
> 
> If you think this or something like it would work, then I guess we could
> talk more about what type of basic tree manipulation code people would
> like to see in Biopython... what are the thoughts on this? 

*Sigh* Dang licensing issues :)  I read with interest the link that Andrew
provided a few posts back, and it is quite good: relatively unbiased, etc. 
Here it is again: http://www.linux.com/news/articles.phtml?aid=7125

However I would really rather keep all the code in mavric under the GPL. 
At the risk of raising hackles I must admit I like the requirement that
modifications to the code be made available-- it appeals to my ideals
about how science should be done, i.e. free and open access to ideas and
improvements (sorry to be so melodramatic :) 

I could be conviced to re-license the phylogeny code and fold it into
biopython if anyone can tell me how this would benefit the project in ways
it could not as a separate 'third-party' module?

Also, if the the phylogeny code did become part of biopython, does this
mean that mavric would thereafter depend on users having biopython (for
the phylogeny libraries)?  Sorry to be dense here. 

I don't want to come across as uncooperative or egotistical (believe me, I
don't have any pretensions about the quality of mavric code-- I mean,
dammit Jim I'm a biologist, not a programmer!)  Thanks for your
understanding. 

--Rick