PUmPER is a framework to build automated pipelines that can perpetually update phylogenetic trees. PUmPER makes use of PHLAWD and RAxML-Light or ExaML to perpetually update Genbank datasets and simultaneously update inferred phylogenetic trees.
You can learn how to setup the system at the wiki page for installation
For an overview on how to use PUmPER, you can follow these Getting-Started tutorials to infer and update trees in standalone or remote mode, or build your first PUmPER phylogenetic pipeline to iteratively build alignments and update trees.
Feel free to post in the PUmPER user group if you have questions regarding installation and usage.
PUmPER is work-in-progress and under continuous development.