[Biopython-dev] Bio.Phylo, Python 3 and Notebooks

[Peter Cock]

On Tue, Oct 7, 2014 at 5:03 PM, Tiago Antao <tra at popgen.net> wrote:
> Hi Peter,
>
> [I suppose you meant a reply all, not just for me?]
>

Yes, oops. Thanks.

>
> On Tue, 7 Oct 2014 16:55:59 +0100
> Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
>> On Tue, Oct 7, 2014 at 4:34 PM, Tiago Antao <tra at popgen.net> wrote:
>> > 2. 14: Do you know where I can find the file other_trees.xml ? Could
>> > not find it
>>
>> It looks like it is generated in an earlier example by parsing
>> phyloxml_examples.xml and then everything except the first
>> tree as other_trees.xml
>>
>> > 3. 15: The same from tree1.dnd
>>
>> Generated in an earlier example by parsing phyloxml_examples.xml
>> and saving the first tree only.
>
> These two actually are an outcome of the failed Python 3 example, they
> should auto-solve as soon as the bug is done.

Great :)

> So, other than the bug itself only this one remains:
>
>> > 4. 42: It seems that paml is not generating a 'lnL max' (just see
>> > the full dictionary appended there)? Potential cookbook bug?
>
> This one is probably for Eric.
>
> Tiago

Thanks,

Peter