ETE is a python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic and other type of trees. It provides a wide range of tree handling methods, node annotation features, programmatic access to the phylomeDB database, and automatic orthology and paralogy prediction methods. In addition, an interactive tree visualization program, as well as a highly customizable tree drawing engine, is included.
A preliminary API to access the new phylomeDB release (v3) is available. Until official integration into the ETE package, you can download and use the API as an independent module (attached). To use it, Salvador Capella has developed an update of the PhylomeDBConnector object that allows to access to phylomeDB mysql server directly.
import PhylomeDB3 p = PhylomeDB3.PhylomeDB3Connector() print p.get_phylomes()
Thanks to Alexis Grimaldi, the ETE package has just been accepted in MacPorts. Now, installing ETE on a mac is as simple as executing: "sudo port install py26-ete2". Note, however, that many dependences will be compiled from source, so it might take a long time the first time you install it.