[Biopython-dev] [Biopython] Bio.Phylo bugs & pain points

[Michiel de Hoon]

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.

--- 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
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