EnsemblCompara GeneTrees: Analysis of complete, duplication aware phylogenetic trees in vertebrates.
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 is made available in a number of formats and will be kept up to date with the Ensembl project.
Footnotes
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- Received October 26, 2007.
- Accepted November 18, 2008.
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This manuscript is Open Access.
- Copyright © 2008, Cold Spring Harbor Laboratory Press
