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

[Tiago Antao]

Hi Peter,

[I suppose you meant a reply all, not just for me?]


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. 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