Kobert Kassian, Salichos Leonidas, Rokas Antonis, Stamatakis Alexandros
Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
Department of Molecular Biophysics and Biochemistry, Yale University Department of Biological Sciences, Vanderbilt University.
Mol Biol Evol. 2016 Jun;33(6):1606-17. doi: 10.1093/molbev/msw040. Epub 2016 Feb 25.
We present, implement, and evaluate an approach to calculate the internode certainty (IC) and tree certainty (TC) on a given reference tree from a collection of partial gene trees. Previously, the calculation of these values was only possible from a collection of gene trees with exactly the same taxon set as the reference tree. An application to sets of partial gene trees requires mathematical corrections in the IC and TC calculations. We implement our methods in RAxML and test them on empirical datasets. These tests imply that the inclusion of partial trees does matter. However, in order to provide meaningful measurements, any dataset should also include trees containing the full species set.
我们提出、实现并评估了一种从一组部分基因树中计算给定参考树上的节点确定性（IC）和树确定性（TC）的方法。以前，只有从与参考树具有完全相同分类单元集的基因树集合中才能计算这些值。将该方法应用于部分基因树集需要在IC和TC计算中进行数学校正。我们在RAxML中实现了我们的方法，并在经验数据集上对其进行了测试。这些测试表明包含部分树确实很重要。然而，为了提供有意义的度量，任何数据集还应包括包含完整物种集的树。
