The Exelixis Lab

Enabling Research in Evolutionary Biology

PUmPER: Phylogenies Updated PERpertually

About PUmPER

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.


The prototype version including documentation is available via Fernando's github repository.

Workflow for an iteration

An initial iteration of the pipeline:

  1. PUmPER constructs an alignment comprising sequences from a clade (from the NCBI taxonomy) and gene regions of interest specified by the user.
  2. The alignment is then used to infer Maximum Likelihood trees in parallel.
  3. The best trees are collected and kept to be re-used as starting trees on the next iteration.