Enabling Research in Evolutionary Biology
Fernando, Stephen Smith, and John Cazes have developed PUmPER, a Ruby framework for phylogenetic analyses. It can be used to build a pipeline that automatically updates reference trees when enough new sequences for the clade of interest appear on GenBank.
The tool uses RAxML-Light to extend trees and Stephen's PHLAWD pipeline to extend alignments by new sequences. The code can be run on stand-alone servers and on cluster systems.
An initial iteration of the pipeline: