[Biopython] Phylo Tree: Need to align Taxa for visual representation

[Eric Talevich]

Asma,

The tree style you want is called a hypermetric tree. The difference is
that all branch lengths are 1 (the default value) in "wrong.png" but in
"correct.png" the total depth of each tip is the same distance from the
root. You could set these branch lengths programmatically to make the sums
work out right; Bio.Phylo doesn't currently implement it. Or you could use
another tree visualization program, like Archaeopteryx (
https://sites.google.com/site/cmzmasek/home/software/archaeopteryx).

-Eric



On Thu, Apr 10, 2014 at 11:29 AM, Asma Riyaz <asmariyaz23 at gmail.com> wrote:

> Hi,
>
> I am using Bio.Phylo package to display a tree, and I am having problems
> representing it the way I want it to be.
>
> Here is my code:
>
>     gs=gridspec.GridSpec(1, 2,height_ratios=[1,1,-2,2]
> ,width_ratios=[1,1,-2,2],hspace=0,wspace=0)
>     phyl_ax=plt.subplot(gs[0])
>     Phylo.draw(tree, axes=phyl_ax, do_show=False,show_confidence=False)
>
>
> With the above code I am able to produce, wrong.png
> I would like the tree to be displayed similar to correct.png (I got this of
> a 3rd party software MEGA) and want to automate the process (hence Phylo)
>
>
> I have tried several of rcParams settings with line specifically but no
> success.
>
> Appreciate any help provided.
> Asma
>
> _______________________________________________
> Biopython mailing list  -  Biopython at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biopython
>
>