### PUmPER (Phylogenies Updated PERperpetually)

PUmPER is a framework to build [automated pipelines](http://sco.h-its.org/exelixis/web/software/put/index.html) that can perpetually update phylogenetic trees. PUmPER makes use of [PHLAWD](http://phlawd.net) and [RAxML-Light](https://github.com/stamatak/RAxML-Light-1.0.5) or [ExaML](https://github.com/stamatak/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](https://github.com/fizquierdo/perpetually-updated-trees/wiki/PUmPER-Setup)

For an overview on how to use _PUmPER_, you can follow these Getting-Started tutorials to infer and update trees in [standalone](https://github.com/fizquierdo/perpetually-updated-trees/wiki/Getting-Started) or [remote](https://github.com/fizquierdo/perpetually-updated-trees/wiki/Getting-Started-Remote) mode, or build your first [PUmPER phylogenetic pipeline](https://github.com/fizquierdo/perpetually-updated-trees/wiki/Standalone-Pipeline) to iteratively build alignments and update trees.

Feel free to post in the [PUmPER user group](http://groups.google.com/d/forum/pumper-user-group) if you have questions regarding installation and usage.

PUmPER is work-in-progress and under continuous development.