TY  - JOUR
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
Y1  - 2009/02/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 327 
EP  - 335 
DO  - 10.1101/gr.073585.107 
VL  - 19 
IS  - 2 
UR  - http://genome.cshlp.org/content/19/2/327.abstract 
N2  - 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. 
ER  -