[Biopython-dev] Release blockers? PAML?

[Eric Talevich]

On Mon, Aug 15, 2011 at 6:04 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> Hi all,
>
> We're about due to make a Biopython release, and I could
> do it early this week - but then I'm away for a fortnight. I am
> fortunate to be attending the BioHackathon 2011 in Kyoto
> next week, http://2011.biohackathon.org/
>
> [...]

> What else should be addressed before the next release?
>
> There are some open bugs, but at first glance nothing
> critical.
>
>
A while ago I pushed a new function, Phylo.draw(). It draws rooted
phylograms much like Phylip's drawgram or ape's plot.tree function. There's
a lot of room for personal preferences here, so I'd appreciate if someone
else could try it out and suggest changes.

Usage:
>>> from Bio import Phylo
>>> tree = Phylo.read('some_tree.nwk', 'newick')
>>> Phylo.draw(tree)

Code:
https://github.com/biopython/biopython/blob/master/Bio/Phylo/_utils.py

The function only takes a few arguments, but since it's based on
matplotlib/pylab, the aesthetics of a plot can easily be changed after the
initial plotting.

If we're happy with it, then I'll add a mention of it to the Tutorial.

While I'm at it, has anyone else used Bio.Applications.PhymlCommandline and
found any issues?

Thanks,
Eric