ETE code is fully functional under IPython Notebook environments, providing inline image visualization.

Inline plots can be generated by calling the tree.render() function with the "%%inline" word as its first argument. This will produce a SVG image of your tree that is directly shown by the browser.

tree.render("%%inline")  

In addition, ETE's Graphical User Interface (GUI) can be launched at any moment for a complete interactive interaction with your tree objects. Just call the tree.show() method available in every node. Browse, explore or even modify your tree. When the GUI is closed, changes will be reflected in your Ipython notebook code.

Layout functions, node faces, styles and all drawing features from ETE treeview module will also be accessible. Phylogenetic trees can even been displayed together with their alignments: