Fig. 4

a–l Quest for Orthologs 2011_04 benchmarks (see [1]) on 66 species across Eukarya, Bacteria and Archaea for ortholog inference methods. Dotted line shows Pareto frontier. Data for graphs are in Additional file 1: Table S1. a, b F-score on SwissTree and TreeFam-A tests. c “Pseudo-F-score” across the two Species Tree Discordance Tests (STDT). d “Pseudo-F-score” across the four Generalized Species Tree Discordance Tests (GSTDT). e–f Agreement of orthologs SwissTree/FreeFam-A trees g-h Benchmarks across the STDT & GSTDT. X-axis: Total fraction of randomly selected genes with predicted orthologs in a predefined set of species for the two STDTs & four GSTDTs respectively. Y-axis: Average (1 – normalised Robinson-Foulds distance) between gene tree for putative orthologs and the known species tree across the two STDT & four GSTD respectively. The four individual GSTDTs and two individual STDTs are shown in Additional file: 1 i-l Zoom in of plots e-h. See Methods section “Ortholog Benchmarking” for details of Quest for Orthologs benchmarks. m Runtime for each method with 4-256 input Fungi proteomes. n Results returned by methods, a multi-species orthogroup is the set of genes descended from a single gene in the last common ancestor of three or more species