We implement two measures for quantifying genealogical concordance in phylogenomic datasets: the gene concordance factor (gCF) and the novel site concordance factor (sCF). For every branch of a reference tree, gCF is defined as the percentage of "decisive" gene trees containing that branch. This measure is already in wide usage, but here we introduce a package that calculates it while accounting for variable taxon coverage among gene trees. sCF is a new measure defined as the percentage of decisive sites supporting a branch in the reference tree. gCF and sCF complement classical measures of branch support in phylogenetics by providing a full description of underlying disagreement among loci and sites. An easy to use implementation and tutorial is freely available in the IQ-TREE software package (http://www.iqtree.org).

中文翻译：

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计算植物统计学数据集一致性因子的新方法。

我们实施了两种方法来量化系统生物学数据集的谱系一致性：基因一致性因子（gCF）和新颖位点一致性因子（sCF）。对于参考树的每个分支，gCF定义为包含该分支的“决定性”基因树的百分比。这项措施已经广泛使用，但是在这里我们介绍了一个软件包，该软件包可以在考虑基因树之间可变的分类单元覆盖率的同时对其进行计算。sCF是一种新的度量标准，定义为在参考树中支持分支的决定性位点的百分比。gCF和sCF通过全面描述基因座和位点之间的潜在分歧，补充了系统发育学中分支支持的经典方法。IQ-TREE软件包（http://www.iqtree.org）中免费提供了易于使用的实现和教程。