E.T.E.

 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. 

Example:

 import PhylomeDB3
 p = PhylomeDB3.PhylomeDB3Connector()
 print p.get_phylomes()