The supplementary figures and legends provide detailed results and analyses from the Quest for Orthologs benchmarks, comparing OrthoFinder with other software tools and online databases. The figures cover: - **Figure S1**: Results of Generalized Species Tree Discordance Tests (GSTDT) and Species Tree Discordance Tests (STDT) for four clades: Vertebrata, Fungi, Eukaryota, and LUCA (Last Universal Common Ancestor). - **Figure S2**: Comparison of OrthoFinder with other software tools in terms of F-score, pseudo F-score, precision & recall, and Robinson-Foulds (RF) distance. - **Figure S3**: Comparison of OrthoFinder with online databases in the same metrics. - **Figure S4**: Deterministic tree reconciliation applied to nodes within a gene tree, analyzing the overlap of species sets under the duplication, loss, deep-coalescence (DLC) model. The legends provide additional context and explanations for the figures, including the methods used and specific metrics such as F-scores, pseudo F-scores, precision, recall, and RF distances. Tables S1a-S1h and S2a-S2b offer detailed accuracy and performance metrics for OrthoFinder and its variants compared to other methods and databases.The supplementary figures and legends provide detailed results and analyses from the Quest for Orthologs benchmarks, comparing OrthoFinder with other software tools and online databases. The figures cover: - **Figure S1**: Results of Generalized Species Tree Discordance Tests (GSTDT) and Species Tree Discordance Tests (STDT) for four clades: Vertebrata, Fungi, Eukaryota, and LUCA (Last Universal Common Ancestor). - **Figure S2**: Comparison of OrthoFinder with other software tools in terms of F-score, pseudo F-score, precision & recall, and Robinson-Foulds (RF) distance. - **Figure S3**: Comparison of OrthoFinder with online databases in the same metrics. - **Figure S4**: Deterministic tree reconciliation applied to nodes within a gene tree, analyzing the overlap of species sets under the duplication, loss, deep-coalescence (DLC) model. The legends provide additional context and explanations for the figures, including the methods used and specific metrics such as F-scores, pseudo F-scores, precision, recall, and RF distances. Tables S1a-S1h and S2a-S2b offer detailed accuracy and performance metrics for OrthoFinder and its variants compared to other methods and databases.