RT Journal
A1 Vilella, Albert J.
A1 Severin, Jessica
A1 Ureta-Vidal, Abel
A1 Heng, Li
A1 Durbin, Richard
A1 Birney, Ewan
T1 EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
JF Genome Research 
JO Genome Research 
YR 2009 
FD February 01 
VO 19 
IS 2 
SP 327 
OP 335 
DO 10.1101/gr.073585.107 
UL http://genome.cshlp.org/content/19/2/327.abstract 
AB 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.