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Standardized benchmarking in the quest for orthologs

Adrian Altenhoff 1 Brigitte Boeckmann 1 Salvador Capella-Gutiérrez 2 Daniel Dalquen 3 Todd Deluca 4 Kristoffer Forslund 5 Jaime Huerta-Cepas 5 Benjamin Linard 6 Cécile Pereira 7 Leszek Pryszcz 8 Fabian Schreiber 9 Alan Sousa da Silva 9 Damian Szklarczyk 10 Clément-Marie Train 11 Peer Bork 12 Odile Lecompte 13 Christian von Mering 1 Ioannis Xenarios 14 Kimmen Sjölander 15 Lars Juhl Jensen 16 Maria J Martin 9 Matthieu Muffato 9 Toni Gabaldon 8 Suzanna E Lewis 15 Paul D Thomas 17 Erik Sonnhammer 18 Christophe Dessimoz 19
Abstract : Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision–recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish standards and an automated web-based service to facilitate orthology benchmarking. Using this service, we characterize 15 well-established inference methods and resources on a battery of 20 different benchmarks. Standardized benchmarking provides a way for users to identify the most effective methods for the problem at hand, sets a minimum requirement for new tools and resources, and guides the development of more accurate orthology inference methods.
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Adrian Altenhoff, Brigitte Boeckmann, Salvador Capella-Gutiérrez, Daniel Dalquen, Todd Deluca, et al.. Standardized benchmarking in the quest for orthologs. Nature Methods, Nature Publishing Group, 2016, 13 (5), pp.425-430. ⟨10.1038/nMeth.3830⟩. ⟨hal-01636892⟩



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