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EnsemblCompara GeneTrees: 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 are made available in a number of formats and will be kept up to date with the Ensembl project.

SUBMITTER: Vilella AJ

PROVIDER: S-EPMC2652215 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature

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EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates.

Vilella Albert J AJ Severin Jessica J Ureta-Vidal Abel A Heng Li L Durbin Richard R Birney Ewan E

Genome research 20081124 2

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 approach ...[more]

PMID: 19029536

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