Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench

Abstract

Orthobench is the standard benchmark to assess the accuracy of orthogroup inference methods. It contains 70 expert curated reference orthogroups (RefOGs) that span the Bilateria and cover a range of different challenges for orthogroup inference. Here we leveraged improvements in tree inference algorithms and computational resources to re-interrogate these RefOGs and carry out an extensive phylogenetic delineation of their composition. This phylogenetic revision altered the membership of 31 of the 70 RefOGs, with 24 subject to extensive revision and a further 7 that required minor changes. We further used these revised and updated RefOGs to provide an assessment of the orthogroup inference accuracy of widely used orthogroup inference methods. Finally, we provide an open-source benchmarking suite to support the future development and use of the Orthobench benchmark.Significance statement Orthogroup inference forms the foundation of comparative genomic analysis. Benchmarks to evaluate performance are essential to enable these methods to be compared and stimulate further method development. Here we present an update to the orthobench benchmark database and provide a comparative performance evaluation of commonly used orthogroup inference methods.Competing Interest StatementThe authors have declared no competing interest.View Full Text