RAxML BlackBox

Alexis Stamatakis and Jacques Rougemont have released RAxML BlackBox, a prototype Web-Server for RAxML which is attached to a 200 CPU-cluster located at the Vital-IT unit of the Swiss Institute of Bioinformatics. You can upload your data and the cluster will mul it over for up to 24 hours, so typically you can analyse alignments up to 1,000 to 1,500 sequences at present. The software itself can handle bigger data sets (see the RAxML page at CIPRES).

Alexis has also doe some work on phylogeny visualisation, including using treemaps. See (doi:10.1007/11573067_29, PDF here).