[BioPython] Phylogenetics trees

[Brad Chapman]

Rick Ree wrote:
>  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. 

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?

Brad