[Biopython] Phylogenetic trees with biopython?

[Peter Cock]

Thank you David,

Peter

P.S. CONTRIB.rst updated:
https://github.com/biopython/biopython/commit/8d87b7c7b2bd9ace973676982ebd0fd03a862768

On Wed, Dec 19, 2018 at 9:05 PM David Winter <david.winter at gmail.com> wrote:
>
> 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/
> blog: sciblogs.co.nz/the-atavism