EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
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DOI：
10.1101/gr.073585.107
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发表时间：
2009-02-01
期刊：
影响因子：
7
通讯作者：
Birney, Ewan
中科院分区：
文献类型：
--
作者：
Vilella, Albert J.;Severin, Jessica;Birney, Ewan
我们已经开发了一个全面的基因定向系统发育资源，EnsemblCompara GeneTrees，基于计算管道来处理聚类，多重比对和树生成，包括处理大基因家族。我们开发了两种新的非基于序列的基因树正确性的指标和基准树的方法。TreeFam的TreeBeST方法在我们手中表现出最好的性能。我们还比较了这种系统发育的方法，聚类方法的直系同源预测，显示了很大的增加，使用系统发育的方法的覆盖范围。所有数据都以多种格式提供，并将与Ensembl项目保持同步。
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.