[Biopython] Bio.Phylo bugs & pain points

[Eric Talevich]

On Sat, Feb 18, 2012 at 11:46 AM, Michiel de Hoon <mjldehoon at yahoo.com>wrote:

> Hi Eric,
>
> > But we do want it to be useful for quickly visualizing a
> > tree as you develop a script or modify a tree
> > interactively in IPython, for example.
>
> Do you need IPython or is regular Python sufficient?
>
> -Michiel.
>

Regular Python plus matplotlib is sufficient. IPython has convenient
integration with pylab, that's all.
-E


>
> --- On Sat, 2/18/12, Eric Talevich <eric.talevich at gmail.com> wrote:
>
> > From: Eric Talevich <eric.talevich at gmail.com>
> > Subject: [Biopython] Bio.Phylo bugs & pain points
> > To: "BioPython Mailing List" <biopython at lists.open-bio.org>,
> "BioPython-Dev Mailing List" <biopython-dev at biopython.org>
> > Date: Saturday, February 18, 2012, 11:34 AM
> > Folks,
> >
> > Since we're coming up on another release of Biopython, I'd
> > like to identify
> > any remaing bugs, pain points, aesthetic flaws, and minor
> > missing features
> > in Bio.Phylo. (And hopefully, fix them before the release.)
> >
> > In particular, the Phylo.draw() function, which plots a
> > rooted phylogram
> > with matplotlib, appeared in the last Biopython release
> > unannounced. There
> > are already many tree-drawing programs that produce
> > beautiful
> > publication-quality graphics, and we're not trying to
> > compete with those.
> > But we do want it to be useful for quickly visualizing a
> > tree as you
> > develop a script or modify a tree interactively in IPython,
> > for example. So
> > -- do the trees drawn by Phylo.draw() look right?
> >
> > Thanks,
> > Eric
> > _______________________________________________
> > Biopython mailing list  -  Biopython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython
> >
>