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

Genome Res. 2009 Feb;19(2):327-35. doi: 10.1101/gr.073585.107. Epub 2008 Nov 24.


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.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

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