@article{Vilella01022009,
author = {Vilella, Albert J. and Severin, Jessica and Ureta-Vidal, Abel and Heng, Li and Durbin, Richard and Birney, Ewan}, 
title = {EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates},
volume = {19}, 
number = {2}, 
pages = {327-335}, 
year = {2009}, 
doi = {10.1101/gr.073585.107}, 
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.}, 
URL = {http://genome.cshlp.org/content/19/2/327.abstract}, 
eprint = {http://genome.cshlp.org/content/19/2/327.full.pdf+html}, 
journal = {Genome Research} 
}