[Biopython] Bio.Phylo.draw_graphviz

[Eric T.]

Yes, it should still work, but keeping track of its dependencies is an
ongoing chore and you may need to do some investigation yourself if it
doesn't work on your system.

The real reason for its deprecation is that the plot it draws is misleading
-- branch lengths are ignored and the distances between nodes in the plot
is arbitrary, per the graphviz layout engine. But it looks like a proper
radial phylogeny at first glance, which could lead to a wrong
interpretation of the data. It would be better for users to create radial
plots with another library like ETE or DendroPy, or just use the simple
rectangular plot produced by Phylo.draw.



On Fri, May 4, 2018 at 10:13 AM, Tiago Antão <tiagoantao at gmail.com> wrote:

> Hi,
>
> I have some old code that uses draw_graphviz, but a recent Biopython is
> saying that it is deprecated. The documentation that I have found on the
> site still refers to draw_graphviz .
>
> A few questions:
> 1. Is it still possible to use graphviz as a backend?
> 2. If so, is there any place to find documentation on it?
>
>
> Thanks a lot,
> Tiago
>
> --
> Tiago Antao
> Scientific and HPC programmer
> http://tiago.org
> https://github.com/tiagoantao/
>
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> Biopython mailing list  -  Biopython at mailman.open-bio.org
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>
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