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

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

Author information

  • 1EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.

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.

PMID:
19029536
[PubMed - indexed for MEDLINE]
PMCID:
PMC2652215
Free PMC Article
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