RT Journal
A1 Vilella, Albert J
A1 Severin, Jessica
A1 Ureta-Vidal, Abel
A1 Durbin, Richard
A1 Heng, Li
A1 Birney, Ewan
T1 EnsemblCompara GeneTrees: Analysis of complete, duplication aware phylogenetic trees in vertebrates.
JF Genome Research 
JO Genome Research 
YR 2008 
FD January 01 
DO 10.1101/gr.073585.107 
SP gr.073585.107 
UL http://genome.cshlp.org/content/early/2008/11/24/gr.073585.107.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 is made available in a number of formats and will be kept up to date with the Ensembl project.