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    <p>I finally got this working. The basic premise is that you're going to use the <code>labels/nodelist</code> to build your <code>node_sizes</code>. This way they correlate properly. I'm sure I'm missing some important options to make the tree look 100% but it appears the node sizes are showing up properly.</p> <pre><code>#basically a stripped down rewrite of Phylo.draw_graphviz import networkx, pylab from Bio import Phylo #taken from draw_graphviz def get_label_mapping(G, selection): for node in G.nodes(): if (selection is None) or (node in selection): try: label = str(node) if label not in (None, node.__class__.__name__): yield (node, label) except (LookupError, AttributeError, ValueError): pass kwargs={} tree = Phylo.read('tree.dnd', 'newick') G = Phylo.to_networkx(tree) Gi = networkx.convert_node_labels_to_integers(G, discard_old_labels=False) node_sizes = [] labels = dict(get_label_mapping(G, None)) kwargs['nodelist'] = labels.keys() #create our node sizes based on our labels because the labels are used for the node_list #this way they should be correct for label in labels.keys(): if str(label) != "Clade": num = label.name.split('-') #the times 50 is just a guess on what would look best size = int(num[-1]) * 50 node_sizes.append(size) kwargs['node_size'] = node_sizes posi = networkx.pygraphviz_layout(Gi, 'neato', args='') posn = dict((n, posi[Gi.node_labels[n]]) for n in G) networkx.draw(G, posn, labels=labels, node_color='#c0deff', **kwargs) pylab.show() </code></pre> <p>Resulting Tree <img src="https://i.stack.imgur.com/0j3VJ.png" alt="alt text"></p>
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    1. POPhylo BioPython building trees
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    1. COActually I also had try that and it does the same thing. I can provide the test file but perhaps it's too large to show it here
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    2. COTry Pastie.org and choose html/xml as the type
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    3. COit's in the question. thank you :)
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