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PEWO: a collection of workflows to benchmark phylogenetic placement

Abstract : Motivation: Phylogenetic placement (PP) is a process of taxonomic identification for which several tools are now available. However, it remains difficult to assess which tool is more adapted to particular genomic data or a particular reference taxonomy. We developed PEWO, the first benchmarking tool dedicated to PP assessment. Its automated workflows can evaluate PP at many levels, from parameter optimisation for a particular tool, to the selection of the most appropriate genetic marker when PP-based species identifications are targeted. Our goal is that PEWO will become a community effort and a standard supportred for future developments and applications of PP. Availability: https://github.com/phylo42/PEWO
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https://hal.archives-ouvertes.fr/hal-02905244
Contributor : Benjamin Linard <>
Submitted on : Thursday, July 23, 2020 - 12:10:39 PM
Last modification on : Friday, January 8, 2021 - 3:06:01 PM
Long-term archiving on: : Tuesday, December 1, 2020 - 5:27:55 AM

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Benjamin Linard, Nikolai Romashchenko, Fabio Pardi, Eric Rivals. PEWO: a collection of workflows to benchmark phylogenetic placement. Bioinformatics, Oxford University Press (OUP), In press, ⟨10.1093/bioinformatics/btaa657⟩. ⟨hal-02905244⟩

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