Skip to content

I. Overview

Jump to bottom
Benjamin Linard edited this page Jul 3, 2020 · 1 revision

PEWO: "Placement Evaluation WOrkflows"

Overview

PEWO compiles a set of worflows dedicated to the evaluation of phylogenetic placement. It focuses on reporting placement accuracy and associated computational costs under different conditions. It can also be used as a tool for optimisation when different references phylogenies are considered for placement.

It is built on Snakemake + Miniconda3 and rely extensively on the Bioconda and Conda-forge repositories, making it portable to most OS supporting Python 3. A specific phylogenetic placement software can be evaluated by PEWO as long as it can be installed on said OS via conda.

Main purposes of PEWO :

  • Evaluate phylogenetic placement accuracy, given a particular reference species tree (and corresponding reference alignment). For instance, one can run PEWO on different trees built for different taxonomic marker genes and explore which markers produce better placements.

  • Given a particular software/algorithm, empirically explore which sets of parameters produces the most accurate placements and for which computational costs. This can be particularly useful when huges volume of sequences are to be placed and one may need to consider a balance between accuracy and scalability (CPU/RAM limitations).

  • For developers, provides a basis to standardize phylogenetic placement evaluation and the establishement of benchmarks. PEWO aims to remove the hassle of re-implementing evaluation protocols that were described in anterior studies. In this regards, any phylogenetic placement developper is welcome to pull new modules in PEWO repository or contact us for future support of their new productions. In this regards, PEWO aims to be a community effort.

Software currently supported by PEWO.

  • EPA(RAxML) (Berger et al, 2010)
  • PPlacer (Matsen et al, 2011)
  • EPA-ng (Barbera et al, 2019)
  • RAPPAS (Linard et al, 2019)
  • APPLES (Balaban et al, 2019)

Currently, (march 2020 2019) there are no other implementations of phylogenetic placement algorithms. If you implement a new method, you are welcome to contact us for requesting future support or you can directly code a new snakemake module and contribute to PEWO via pull requests (see documentation for contribution rules).

Clone this wiki locally