[Biopython] Phylogenetic trees with biopython?

[Peter Cock]

Dear David,

Back in 2009 you kindly made a couple of contributions to Biopython's
EMBOSS wrappers (and some test cases too, and documentation IIRC):

https://github.com/biopython/biopython/commit/f04c083482899a4ec330cae2fad158dc6f0fd131

https://github.com/biopython/biopython/commit/d9e8972b3956e4c30dc7afd9049dc13283865b60

Would you agree to dual license all your contributions to Biopython
under the user's choice of the current "Biopython License Agreement"
and the standard "BSD 3-Clause License"? A reply to our public
mailing list or as comment on this GitHub issue would suffice as a
public record: https://github.com/biopython/biopython/issues/898

Thank you,

Peter

P.S. I see you are now on GitHub, so on a related note, may I
update your CONTRIB listing entry to point there?

https://github.com/dwinter

On Tue, Sep 1, 2009 at 11:38 PM David Winter
<winda002 at student.otago.ac.nz> wrote:
>
>
> > David - I would prefer we also put your new wrappers in
> > Bio.Emboss.Applications, and would be happy to look at adding
> > those to CVS now that Biopython 1.51 is out (I had forgotten
> > about them actually - so thanks for the reminder).
> >
> > Peter
>
> Hi Peter,
>
> I'd almost forgotten about them myself! I only put them in their own
> module because I had the PhyML wrapper as well and that's not an
> EMBOSS application.
>
>   I suspect a wrapper for PhyML is probably not going to be widely
> useful (a normal run lasts at least several hours and most people will
> want to look over their alignments by eye before they set it off). So
> I'll move the phylip ones into Emboss.Applications and gather a few
> thoughts about other phylogenetic software including PhyML and see
> what the dev list thinks about them.
>
> david
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython