duplication-aware phylogenetic trees in vertebrates

We have developed a comprehensive gene orientated phylogenetic resource, EnsemblCompara GeneTrees, based on a computational pipeline to handle clustering, multiple alignment, and tree generation, including the handling of large gene families. We developed two novel non-sequence-based metrics of gene tree correctness and benchmarked a number of tree methods. The TreeBeST method from TreeFam shows the best performance in our hands. We also compared this phylogenetic approach to clustering approaches for ortholog prediction, showing a large increase in coverage using the phylogenetic approach. All data are made available in a number of formats and will be kept up to date with the Ensembl project. [Supplemental material is available online at www.genome.org.] The use of phylogenetic trees to describe the evolution of bi-ological processes was established in the 1950s (Hennig 1952) and remains a fundamental approach to understanding the evolution of individual genes through to complete genomes; for example, in the mouse (Mouse Genome Sequencing Consortium 2002), rat (Gibbs et al. 2004), chicken (International Chicken Genome Se-quencing Consortium 2004), and monodelphis (Mikkelsen et al