[Biopython] Bio.Phylo.draw_graphviz

[Peter Cock]

I've tried to capture this on the website,

https://github.com/biopython/biopython.github.io/commit/5b6800872c7ecdb58f8ec90518e464515cab71df

However, I think it would be best if you could review that - I'm unsure
which function made the images shown etc.

Peter


On Sat, May 5, 2018 at 7:13 AM, Eric T. <eric.talevich at gmail.com> wrote:
> 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/
>>
>> _______________________________________________
>> Biopython mailing list  -  Biopython at mailman.open-bio.org
>> http://mailman.open-bio.org/mailman/listinfo/biopython
>
>
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython