[Biopython] Phylogenetic trees with biopython?

[David Winter]

Hi Peter et al.

Very happy to add the BSD 3-clause license, and makes sense to have the
CONTRIB info point to my github.

Thanks,
David

On Tue, Dec 18, 2018 at 11:23 PM Peter Cock <p.j.a.cock at googlemail.com>
wrote:

> 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
>


-- 
David Winter
Postdoctoral Research Fellow
Institute of Fundamental Sciences
Massey University
Palmerston North 4442
New Zealand

ph: +64 0204 119 2692
w: www.david-winter.info
lab: http://massey.genomicus.com/ <http://cartwrig.ht/lab/>
blog: sciblogs.co.nz/the-atavism
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