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

2008; Cold Spring Harbor Laboratory Press; Volume: 19; Issue: 2 Linguagem: Inglês

10.1101/gr.073585.107

1549-5469

Albert J. Vilella, Jessica Severin, Abel Ureta-Vidal, Heng Li, Richard Durbin, Ewan Birney,

Chromosomal and Genetic Variations

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.