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      EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.

      Genome research

      Algorithms, Animals, Computational Biology, methods, Gene Duplication, Humans, Models, Biological, Multigene Family, Phylogeny, Sequence Homology, Software, Synteny, Vertebrates, classification, genetics

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          Abstract

          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.

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          Author and article information

          Journal
          10.1101/gr.073585.107
          2652215
          19029536

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