The authors have developed EnsemblCompara GeneTrees, a comprehensive gene-oriented phylogenetic resource for vertebrates. This resource uses a computational pipeline to handle clustering, multiple alignment, and tree generation, including the handling of large gene families. The pipeline includes two novel non-sequence-based metrics to assess gene tree correctness and benchmarks several tree methods. The TreeBEST method from TreeFam is found to perform best. The phylogenetic approach is compared to clustering approaches for ortholog prediction, showing a significant increase in coverage. The data are made available in various formats and will be updated with the Ensembl project. The paper details the motivation, implementation, and benchmarking of the method, as well as the display and access methods for these trees. The authors also discuss the robustness and efficiency of the pipeline, the comparison of their results with other orthology sets, and the benefits of the phylogenetic information for gene family analysis and functional annotation.The authors have developed EnsemblCompara GeneTrees, a comprehensive gene-oriented phylogenetic resource for vertebrates. This resource uses a computational pipeline to handle clustering, multiple alignment, and tree generation, including the handling of large gene families. The pipeline includes two novel non-sequence-based metrics to assess gene tree correctness and benchmarks several tree methods. The TreeBEST method from TreeFam is found to perform best. The phylogenetic approach is compared to clustering approaches for ortholog prediction, showing a significant increase in coverage. The data are made available in various formats and will be updated with the Ensembl project. The paper details the motivation, implementation, and benchmarking of the method, as well as the display and access methods for these trees. The authors also discuss the robustness and efficiency of the pipeline, the comparison of their results with other orthology sets, and the benefits of the phylogenetic information for gene family analysis and functional annotation.