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.
Given that ETE's community has started to spread, I think a discussion list would make sense to tackle doubts and problems. So, here we have a public googlegroup: groups.google.com/group/etetoolkit. Feel free to join us and raise your questions! (Note that important news and bug fixes will be also announced in the list.)
Organized by the Gabaldon's lab at CRG and The Gulbenkian Training Programme in Bioinformatics (GTPB)
Location: Oerias, Portugal. Dates: from 23rd June to 25th June, 2010
Jaime Huerta-Cepas, Joaquín Dopazo and Toni Gabaldón. ETE: a python Environment for Tree Exploration. BMC Bioinformatics 2010, 11:24. [ link ]