[Biopython-dev] [Biopython - Feature #3260] (Closed) Draw a Bio.Phylo tree as a phylogram

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Thu Jul 14 03:02:35 UTC 2011

Issue #3260 has been updated by Eric Talevich.

Status changed from New to Closed
% Done changed from 0 to 100


Folks: lemme know how this works for you.
Feature #3260: Draw a Bio.Phylo tree as a phylogram

Author: Eric Talevich
Status: Closed
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 

Bio.Phylo should be able to draw a decent tree. This means a standard phylogram, with accurate branch lengths, labels for taxa and any internal nodes that have them, and support values -- like Phylip's "drawtree" does.

The two existing functions don't quite suffice: draw_graphviz ignores branch lengths, though it's nice for unrooted trees; draw_ascii looks more like a typical phylogram, but it's ascii art and can't display internal node labels or support values (or large trees).

I wrote a function to do this, based on the algorithm in draw_ascii. It uses matplotlib for display. I tested it on all the trees under Tests/Nexus and Tests/PhyloXML; it's nice.

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